AGOURON PHARMACEUTICALS INC
10-K, 1996-09-19
PHARMACEUTICAL PREPARATIONS
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<PAGE>
                 UNITED STATES SECURITIES AND EXCHANGE COMMISSION
                              Washington, D.C. 20549
                                      FORM 10-K

(Mark One)
_X_ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE
    ACT OF 1934 [FEE REQUIRED] 

For the fiscal year ended June 30, 1996
                                        OR
   TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES
   EXCHANGE ACT OF 1934 [NO FEE REQUIRED] 
For the transition period from.............  to  ........................... 
Commission file number 0-15609

                          Agouron Pharmaceuticals, Inc. 
             (Exact name of registrant as specified in its charter) 

           California                                        33-0061928
(State or other jurisdiction of                           (I.R.S. Employer
 incorporation or organization)                          Identification No.) 

10350 North Torrey Pines Road, La Jolla, California           92037-1020
    (Address of principal executive offices)                  (Zip Code) 

Registrant's telephone number, including area code  (619) 622-3000

Securities registered pursuant to Section 12(b) of the Act:     None

Securities registered pursuant to Section 12(g) of the Act: 

                         Common Stock, without par value
                                 (Title of class) 

     Indicate by check mark if disclosure of delinquent filers pursuant to
Item 405 of Regulation S-K is not contained herein, and will not be 
contained, to the best of registrant's knowledge, in definitive proxy or
information statements incorporated by reference in Part III of this Form
10-K or any amendment to this Form 10-K.  [  ] 

     Indicate by check mark whether the registrant (1) has filed all reports
required to be filed by Section 13 or 15(d) of the Securities Exchange Act
of 1934 during the preceding 12 months and (2) has been subject to such
filing requirements for the past 90 days.  Yes__X__ No _____

     On September 13, 1996, the aggregate market value of the voting stock 
held by nonaffiliates totaled approximately $530,563,000 based on the 
closing stock price as reported by The Nasdaq Stock Market. 

     On September 13, 1996, there were 13,500,134 shares of common stock, 
without par value, of the registrant issued and outstanding. 

                        DOCUMENTS INCORPORATED BY REFERENCE

     The registrant's definitive proxy statement to be prepared pursuant to 
Regulation 14A and filed in connection with solicitation of proxies for its 
Annual Meeting of Stockholders, to be held on November 7, 1996, is 
incorporated by reference into Part III of this Form 10-K. 
<PAGE>
                                     PART I

Item 1.      BUSINESS

     Except for the historical information contained herein, the following 
"Business" section contains forward-looking statements that involve risks
and uncertainties. The Company's actual results could differ materially from
those discussed here. Factors that could cause or contribute to such 
differences include, but are not limited to, those discussed in the
"Business" section and Exhibit 99 to this Form 10-K. 

General

     The Company was organized and incorporated in California in June 1984. 
Agouron is a pioneer and leader in technologies that enable the atom-by-atom 
design of novel synthetic drugs based upon the molecular structures of 
target proteins which play key roles in human disease.  The Company is 
conducting phase II/III clinical trials of two drugs generated by these 
design technologies:  VIRACEPT (TM) (nelfinavir mesylate) for treatment of 
HIV infection and THYMITAQ (TM) (AG337) for treatment of solid malignant 
tumors. 

In addition, eleven preclinical programs are in progress for discovery or 
development of other new drugs in the fields of cancer, viral disease, and 
inflammatory disease.  The Company's business currently consists of one 
business segment, the operations of which are described below. 

     Agouron's goal is to become profitable from the sale of differentiated 
drugs generated principally from its own drug discovery and development 
efforts.  To augment its technical capabilities, to enhance the likelihood 
of successful commercialization of its products and to offset some of its 
operating costs, the Company has entered into collaborative research and 
development arrangements with other companies.  However, consistent with its 
commercial goal, the Company has generally retained significant commercial 
rights in drugs developed in its collaborative research and development 
programs funded in whole or in part by other companies.  The Company 
anticipates that its successfully developed products will be commercialized 
both through its own direct sales and marketing activities in certain 
pharmaceutical markets, when appropriate, and through manufacturing and 
marketing relationships with other pharmaceutical firms. 

     The Company's common stock account has evolved through a series of 
public offerings and private placements of its common and preferred stock 
and the exercise of various warrants and employee stock options.  Five 
public offerings (calendar 1987, 1989, 1991, 1995 and 1996) generated net 
proceeds of approximately $212,400,000 through the issuance of approximately 
9,894,000 shares.  The most recent public offering raised approximately 
$77,674,000 through the issuance of 2,735,000 shares.  Private placements of 
both common and preferred stock have generated approximately $17,090,000 in 
net proceeds and the issuance of approximately 2,763,000 shares.  Private 
placements in fiscal 1993 generated $6,000,000 through the issuance of 
approximately 312,000 shares.  The exercise of warrants and employee stock 
options (including employee stock purchase plan transactions) have generated 
proceeds of approximately $7,190,000 and the issuance of approximately 
810,000 shares. 

Narrative Description of Business

     Agouron is developing innovative drugs for treatment of cancer, HIV 
infection and other serious diseases and has expended approximately 
$191,000,000 on research and development since its inception. 
<PAGE>
     VIRACEPT, an orally administered inhibitor of the enzyme HIV protease, 
is the subject of pivotal phase II/III clinical studies evaluating the anti-
HIV activity and safety of two alternative doses of the drug for six months 
principally in combination with approved anti-HIV drugs in more 
than 700 HIV-infected subjects in the United States. If successful, these 
studies could lead to the submission of a New Drug Application ("NDA") to 
the U.S. Food and Drug Administration ("FDA") for VIRACEPT in the first 
quarter of calendar 1997. In a series of shorter, smaller, pilot phase II 
studies, comparable doses of VIRACEPT taken alone or in combination with 
other anti-HIV drugs produced profound reductions in the amount of HIV 
detectable in the blood of patients and significant increases in their CD4+ 
T cell counts. VIRACEPT was reported to be safe and well tolerated in the 
pilot studies. Agouron is presently preparing to market and sell VIRACEPT in 
North America upon its approval by the FDA. 

     Agouron is developing VIRACEPT in collaboration with the pharmaceutical 
division of Japan Tobacco Inc. ("JT"). In collaboration with JT, Agouron is 
also engaged in the discovery of drugs for treatment of infections caused by 
hepatitis C and by herpes viruses. Under agreements with JT, Agouron retains 
exclusive commercial rights to these anti-viral products in the 
United States, Canada and Mexico, generally subject to the payment either of 
royalties or a share of profits to JT. 

     THYMITAQ, an inhibitor of the enzyme TS, is presently the subject of 
phase II/III clinical studies evaluating the drug as a chemotherapeutic 
agent for treatment of malignant solid tumors associated with cancer of the 
liver (hepatocellular carcinoma) and cancer of the head/neck. Previously, 
six small phase II clinical studies evaluated 5-day courses of treatment 
with THYMITAQ administered intravenously in patients with malignant solid 
tumors associated with cancer of the colon, lung, liver, pancreas, prostate 
or head/neck. Tumor reductions of greater than 50% were observed in patients 
with head/neck cancer, liver cancer, lung cancer and colon cancer. 
Stabilization of disease was observed in a majority of the remaining 
evaluable patients in all groups studied. An oral formulation of THYMITAQ is 
also being developed by the Company. If successful, the phase II/III pivotal 
clinical trials could lead to submission of a NDA for THYMITAQ late in 
calendar 1997 or in calendar 1998. Agouron intends to engage in the sales 
and marketing of THYMITAQ in North America upon its approval by the FDA. 

     In June 1996, Agouron signed a binding letter of intent with Hoffmann-
La Roche Inc. and F. Hoffmann-La Roche Ltd., subsidiaries of Roche Holdings 
Ltd. ("Roche"), providing for the collaborative development and 
commercialization of THYMITAQ and of the Agouron anti-cancer compound 
designated AG3340 currently under preclinical development. Under provisions 
of this letter of intent, Agouron is to receive initial license fees and 
additional development milestone payments from Roche. Roche has agreed to 
bear 80% of future costs of developing these drugs. Agouron and Roche will 
cooperatively market the two compounds for cancer indications and share 
profits in North America, while Roche has exclusive marketing rights for 
cancer indications to these compounds outside of North America, subject to 
the payment of royalties to Agouron. Roche also is to provide annual 
research funding support and subsequent milestone payments to Agouron for 
similar commercial rights for all indications in compounds which are 
generated in a collaborative research program focused on cell cycle control. 
<PAGE>
Research and Development Programs

     Agouron's research and development programs concentrate in three areas 
of human disease:  cancer, viral disease and inflammatory disease.  All of 
Agouron's drug discovery programs apply the Company's core technologies for 
the atom-by-atom design of small synthetic drug molecules based upon the 
three dimensional molecular architecture of proteins that play key roles in 
human disease.  The following table outlines the Company's portfolio of 
preclinical and clinical research and development programs.  Some of these 
programs are being pursued by Agouron independently while others are being 
undertaken in collaboration with other companies. 
<TABLE>
<CAPTION>
<S>               <S>           <S>               <S>                <S>
Program           Indication    Protein Target    Development Stage  Partner
- -------           ----------    --------------    -----------------  -------

Cancer
 
 THYMITAQ-i.v.    Solid Tumors      TS                Phase II/III    Roche
 THYMITAQ-oral    Solid Tumors      TS                Phase I         Roche
 AG2034           Solid Tumors      GART              Phase I         None
 AG3340           Metastasis        MMPs              Preclinical     Roche
 AICART           Solid Tumors      AICART            Research        None
 cdk4             Solid Tumors      cdk4              Research        Roche
 VEGF Receptor    Solid Tumors      kdr               Research        None

Viral Disease

 VIRACEPT         HIV Infection     HIV Protease      Phase II/III    JT
 Rhinovirus       Common Cold       RhV 3C Protease   Research        None
 Cytomegalovirus  CMV Infection     CMV Protease      Research        JT
 Herpes simplex   Herpes Infection  HSV-1 Protease    Research        JT
 Hepatitis C      Viral Diseases    Hepatitis C Protease    Research  JT

Inflammatory Disease

 MMP              Arthritis         MMPs              Research        Roche
 AICART           Inflammation      AICART            Research        None
</TABLE>

Cancer

     Overview

     The development of new drugs for treatment of cancer is a primary 
scientific and commercial focus of the Company. Cancer is the second leading 
cause of death in the United States and most developed nations. While much 
progress has been made in the treatment of certain forms of cancer, most 
existing anti-cancer drugs display limited efficacy and significant 
toxicities that restrict their clinical usefulness. As a result, there 
remains a critical need for anti-cancer drugs which are less toxic and more 
efficacious either as tumoricidal (tumor-killing) or tumoristatic (tumor-
controlling) agents. 

     Agouron believes that the next generation of agents for treatment of 
the most common human cancers should have a target other than DNA, should be 
more capable of evading drug resistance and should retain activity against 
non-proliferating tumor cells. The Company's anti-cancer drug discovery and 
development programs are aimed at meeting these criteria by focusing on the 
discovery and development of inhibitors of the following enzymes: 
<PAGE>
thymidylate synthase (TS); glycinamide ribotide formyltransferase ("GART"); 
matrix metalloproteases (MMPs); aminoimidazole carboxamide ribonucleotide 
formyltransferase ("AICART"); cyclin dependent kinase 4 ("cdk4"); and a 
receptor for Vascular Endothelial Growth Factor ("VEGF"). Three of these 
enzyme targets (TS, GART and AICART) have a common structural motif that 
permits lead inhibitors from one program to be useful potentially in others. 

     TS Inhibitors: THYMITAQ

     The enzyme TS catalyzes a critical step in the synthesis of DNA and is 
especially crucial to cancer cells undergoing uncontrolled proliferation. 
Independent research has established that the efficacy of the anti-tumor 
drug 5-fluorouracil derives from its ability to inactivate TS. Inhibition of 
TS kills tumor cells by inducing programmed cell death -- a form of natural
cellular suicide by which normal cell growth is usually regulated. It has 
been Agouron's goal to design highly specific inhibitors of TS that overcome 
the several limitations of 5-fluorouracil. In particular, Agouron has 
focused on the design of TS inhibitors of novel chemical character that it 
believes may be capable of penetrating fatty membranes and tissues, 
circumventing some of the more common forms of drug resistance and passing 
into and out of cells by passive diffusion, allowing for much greater 
clinical control of toxicity and for a broader spectrum of anti-tumor 
activity. Agouron's lead compound in the TS program, THYMITAQ, is in phase 
II/III clinical testing. 

     Phase I studies of THYMITAQ initially conducted at the medical hospital 
of the University of Newcastle upon Tyne in England, under the sponsorship 
of the British Cancer Research Campaign, evaluated first an intravenous 
("i.v.") formulation and then an oral formulation of THYMITAQ. In these
phase I studies, which were ultimately extended into the United States and 
involved a total of 45 advanced cancer patients, the maximum tolerated 5-day 
dose of THYMITAQ was determined through a series of dose escalations. On the 
basis of these studies, a dose of 1000 mg/m/day was determined to be 
appropriate for phase II efficacy studies. The phase I studies demonstrated 
that THYMITAQ i.v. was well tolerated: at the maximum tolerated dose, the 
predominant toxicities were determined to be myelosuppression (suppression 
of bone marrow activity) of short duration and mucositis (mouth sores) which 
could frequently be mitigated with a simple mouthwash. A subsequent phase I 
study involving 32 patients in England demonstrated that oral administration 
of THYMITAQ resulted in a pharmacokinetic and safety profile similar to that 
of the i.v. formulation. 

     The Company has conducted six small phase II trials of the i.v. 
formulation of THYMITAQ. The six studies have evaluated 5-day courses of 
treatment with THYMITAQ in patients with malignant solid tumors associated 
with cancer of the colon, lung, liver, pancreas, prostate or head/neck. 
Tumor reductions of greater than 50% were observed in patients with 
head/neck cancer, liver cancer, lung cancer and colon cancer. Stabilization 
of disease was observed in a majority of the remaining evaluable patients in 
all groups studied. Of 19 evaluable patients with head/neck cancer, four 
experienced reductions in tumor mass greater than 50%, including two 
patients with reductions of 100%. Of 18 patients with hepatocellular (liver) 
cancer, two experienced tumor reductions greater than 50%; two others 
experienced tumor reductions sufficient to permit surgical removal of tumors 
previously deemed to be inoperable. 

     Pivotal phase II/III clinical trials have recently been initiated at 
several clinical sites in the United States for evaluation of THYMITAQ as a 
single agent treatment in cancer of the head/neck and in liver cancer. For 
treatment of head/neck cancer, THYMITAQ is being compared to the 
chemotherapeutic agent methotrexate in patients who have failed first-line 
therapy. For treatment of liver cancer, THYMITAQ is being evaluated in a
non-comparative clinical trial, as no drugs are currently approved for use
as single agents in this disease. Complete enrollment of these studies is
expected to require several months. The Company intends to supplement the 
U.S. clinical trials of THYMITAQ by opening additional clinical studies in 
Europe (head/neck cancer) and in Asia (liver cancer). If enrolled in a 
timely manner and if successful, the pivotal trials could permit the Company 
to file a NDA  for THYMITAQ in calendar 1998. 
<PAGE>
     The binding letter of intent signed by Agouron and Roche in June 1996
provides for the collaborative further development and commercialization for 
cancer indications of THYMITAQ. Under provisions of this letter of intent, 
Agouron is to receive license fees and subsequent development milestone 
payments from Roche. Roche has agreed to bear 80% of future costs of 
developing THYMITAQ. Agouron and Roche will cooperatively market THYMITAQ 
for cancer indications and share profits from sales of the drug in North 
America. Roche has exclusive marketing rights to THYMITAQ for cancer 
indications outside North America, subject to possible co-promotion rights
and the payment of royalties to Agouron. 

     GART Inhibitors: AG2034

     An Agouron research program has resulted in the design of AG2034. 
AG2034 is a potent, selective inhibitor of glycinamide ribonucleotide 
transformylase (GART) -- a key enzyme in the biochemical pathway through 
which tumor cells synthesize purines, essential components of DNA. With the 
exception of liver cells, all normal human tissues obtain purines through an 
alternative pathway (the purine salvage pathway). The Company believes that 
inhibitors of GART will show a high degree of selectivity for tumor cells 
and less significant bone marrow toxicity than other chemotherapeutic 
agents. 

     AG2034 has demonstrated preclinical anti-tumor activity against a broad 
panel of tumor types in preclinical models at various dosing schedules. In 
cell culture experiments, AG2034 selectively kills tumor cells missing 
certain cell cycle checkpoints, but is inactive against cells with normal 
checkpoint functions. Because it has become technically possible to 
determine whether biopsied tumor cells are deficient in checkpoint 
functions, the Company believes that physicians may be able to determine in 
advance of treatment which tumors are most likely to respond to AG2034. 

     Agouron has completed initial chemical scale-up of AG2034 and initial 
preclinical toxicology studies. An Investigational New Drug Application has 
been reviewed by the FDA, and Agouron has been cleared to intiate phase I 
clinical studies of AG2034 in the fall of calendar 1996.  The Company 
presently retains all commercial rights to any compounds resulting from this 
program. 

     MMP Inhibitors: AG3340

     Independent research has shown MMPs to be involved in many disease 
states. Certain MMPs have been associated with tumor growth, the metastasis 
of tumor cells to secondary sites within the body and the growth of new 
blood vessels (angiogenesis) through which tumor cells obtain nutrients and 
growth factors. The Company believes that MMPs represent a new opportunity 
for the discovery of novel tumoristatic agents. The Company further believes 
that orally active inhibitors of certain combinations of MMPs, but not of 
all MMPs, are most likely to have the optimal safety and efficacy profiles 
of superior tumoristatic agents. 

     A three-year program of drug discovery undertaken by Agouron in 
collaboration with Roche ("Roche 1993") has resulted in the selection of the 
compound designated AG3340 for development by the Company as an anti-cancer 
agent. AG3340 selectively inhibits the MMPs known as Gelatinase A and B, 
Stromelysin-1 and Collagenase-3, but is relatively inactive against 
Fibroblast Collagenase. In preclinical tests, AG3340 has demonstrated 
excellent anti-tumor in vivo activity following oral administration in both 
mouse and human tumor xenograft models. Significant tumor growth delays in 
all models and significant reductions of spontaneous metastases in the mouse 
Lewis lung model have been reported at recent scientific meetings. 
Toxicology studies are currently underway to support initiation of phase I 
clinical studies of AG3340 late in calendar 1996. 

     Other compounds from the Roche 1993 collaboration on MMP inhibitors are 
the subjects of preclinical evaluation including certain compounds being 
evaluated by Roche as agents for treatment of arthritis. 
<PAGE>
     The binding letter of intent signed by Agouron and Roche in June 1996 
provides for the collaborative further development and commercialization for 
cancer indications of AG3340 and certain other compounds. Under provisions 
of this agreement, Agouron is to receive license fees and subsequent 
development milestone payments from Roche. Roche has agreed to bear 80% of 
future costs of developing AG3340. Agouron and Roche will cooperatively 
market AG3340 for cancer indications and share profits from sales of the 
drug in North America. Roche has exclusive marketing rights to AG3340 for 
cancer indications outside North America, subject to certain co-promotion 
rights and the payment of royalties to Agouron. 

     AICART Inhibitors

     The enzyme AICART catalyzes a rate-determining step in the purine 
biosynthetic pathway and represents a second target for anti-cancer drugs 
which are active by virtue of their anti-purine effects. Research has shown 
that inhibiting the rate-limiting enzyme in such a pathway produces the most 
significant effects on the growth of cells dependent on that pathway. The 
scientific rationale for GART as a target for new anti-tumor drugs applies 
equally to AICART. Agouron scientists believe that two inhibitors of the 
purine pathway -- an inhibitor of GART and an inhibitor of AICART -- may be 
highly synergistic in producing anti-tumor activity when administered in 
combination. 

     The Company's scientists have solved the three-dimensional structure of 
AICART and are engaged in design, synthesis and evaluation of AICART 
inhibitors intended to be efficacious in the treatment of cancer. The 
Company presently retains all commercial rights to any compounds resulting 
from this program. 

     Cell Cycle Control: cdk4

     Cyclin dependent kinases are enzymes that play roles in regulating the 
transitions between phases in the life cycles of all cells. A member of this 
family of enzymes known as cdk4 has been implicated by independent research 
in driving cells from a quiescent phase to the highly proliferative phase 
characteristic of malignancies -- particularly in familial melanomas, 
esophageal carcinomas and pancreatic cancers. Agouron has been engaged in a 
drug discovery program aimed at the design of selective small molecule drugs 
with the potential to inhibit the activity of cdk4 and therefore block the 
transition of cancer cells into their proliferative phase. 

     Under provisions of the binding letter of intent signed by Agouron and 
Roche in June 1996, Roche is to pay to Agouron annual research funding for 
three years in support of the cdk4 program. Commercial rights for all 
indications in compounds which are generated in the program are similar to 
those which Roche has for the MMP inhibitor AG3340. 

     VEGF Receptor

     The process known as angiogenesis, the formation of new blood vessels, 
is a key factor in the maintenance and progression of several disease states 
including the metastasis of malignant tumors. The ability of cancer cells to 
carry out angiogenesis depends in part upon the activity of a protein known 
as Vascular Endothelial Growth Factor (VEGF) which, by binding to a receptor 
known as kdr, triggers the growth of endothelial cells. Agouron is engaged 
in a drug discovery program whose objective is the design of drugs that 
block the kdr receptor for VEGF and therefore compromise the ability of 
tumors to carry out a key process in angiogenesis. The Company presently 
retains all commercial rights to any compounds resulting from this program. 
<PAGE>
Viral Disease

     Overview

     The development of new drugs for the treatment of certain viral 
diseases is another scientific and commercial focus of the Company. The 
Company is presently conducting programs aimed at discovery and/or 
development of four classes of anti-viral drugs which block viral proteases, 
enzymes required by several families of pathogenic viruses to carry out 
replication and infection. Agouron's anti-viral drug programs include HIV 
protease inhibitors (VIRACEPT), rhinovirus 3C protease inhibitors, herpes 
virus protease inhibitors and hepatitis C protease inhibitors. Agouron is 
developing certain of its anti-viral drugs in collaboration with JT. 

     HIV Protease Inhibitor: VIRACEPT

     Research and development of drugs for treatment of HIV infection and 
AIDS in the pharmaceutical industry has thus far produced both successes and 
disappointments. Initially, scientists were optimistic that blocking the 
essential HIV enzyme reverse transcriptase ("RT") would prove sufficient to 
defeat the replication of HIV and curb the progression of HIV infection to 
AIDS. As a result of research and development efforts by several 
pharmaceutical companies, several RT inhibitors are now approved for use in 
the United States. However, the clinical usefulness of this first generation 
of anti-HIV drugs has generally been limited by their toxicity and by the 
ability of HIV to mutate into forms that are resistant to them. For this 
reason, it has been a high priority at Agouron, as well as at other 
pharmaceutical companies, to discover and develop new anti-HIV drugs that 
work by a mechanism of action other than inhibition of RT. 

     Inhibitors of the enzyme HIV protease are widely regarded as one of the 
most promising new classes of anti-HIV drugs. HIV protease is an enzyme that 
performs an essential role in the infectious cycle of HIV. Research shows 
that inhibition of the protease enzyme renders HIV unable to form new 
infectious virus. Three HIV protease inhibitors have been approved by the 
FDA for marketing in the United States during the last year. Agouron 
believes that its HIV protease inhibitor, VIRACEPT, has properties that will 
permit it to compete effectively with these approved drugs. 

     A series of small, short-term pilot phase II clinical studies has been 
completed evaluating the safety and acute anti-HIV efficacy of several daily 
oral doses of VIRACEPT administered orally to HIV-infected subjects. In
these studies, VIRACEPT taken alone, in a two-day combination with stavudine
(d4T) or in a three-drug combination with zidovudine (AZT) and iamivudine 
(3TC), produced profound decreases in the amount of HIV detectable in the 
blood of patients and significant increases in their CD4+ T cell counts. 
Pivotal phase II/III clinical studies of daily doses of 500 mg and 750 mg of 
VIRACEPT administered three times daily in a tablet formulation, principally 
in combination with other anti-HIV drugs, are currently in progress at a 
large number of sites in the United States. In the pilot phase II studies, 
such doses of VIRACEPT were safe and well tolerated, the most common side-
effect being loose stool/diarrhea. 

     If the current phase II/III clinical trials of VIRACEPT are completed 
on a timely basis and if results from these trials are satisfactory, Agouron 
plans to file a NDA in the first quarter of calendar 1997 and, if the NDA is 
approved on a timely basis, to launch VIRACEPT in North America later in 
calendar 1997. However, there can be no assurance that any of these events 
will occur. 
<PAGE>
     Rhinovirus 3C Protease Inhibitors

     Rhinoviruses are believed to be the single most frequent cause of the 
common cold. While rhinovirus infections are a periodic annoyance to most 
normal individuals, they produce more severe and prolonged symptoms in 
people with asthma, emphysema and chronic obstructive pulmonary disease. The 
family of rhinoviruses has eluded attempts to develop a useful vaccine 
because it contains more than 100 serotypes. However, all known strains of 
rhinoviruses depend on a critical enzyme, the 3C protease, at several stages 
of their life-cycle for production of new infectious viruses. It has been 
shown both by independent research and by Agouron scientists that 
inactivating this enzyme halts rhinovirus production in vitro. Because there 
is no known natural counterpart for the 3C protease enzyme in humans, 
Agouron scientists believe that the potential for toxicity from selective 
inhibitors of the rhinovirus 3C protease is low. 

     Agouron's rhinovirus protease research has resulted in the design of 
potent, selective rhinovirus 3C protease inhibitors currently being 
evaluated in preclinical pharmacological studies of anti-viral activity, 
cellular toxicity and oral bioavailability. It is the Company's goal to 
select one such inhibitor for development within 12 months. The Company 
presently retains all commercial rights to any compounds resulting from this
 program. 

     CMV and HSV-1 Protease Inhibitors

     Among the most clinically significant members of the family of herpes 
viruses are herpes simplex virus-1 (HSV-1) and cytomegalovirus (CMV). Like 
HIV and rhinoviruses, HSV-1 and CMV each contain a protease enzyme essential
for virus maturation and infection. Agouron believes that these protease 
enzymes represent targets for a new class of anti-viral drugs with the 
potential for low toxicity. Agouron scientists have recently solved the
three-dimensional molecular structure of the targeted protease enzyme from 
CMV and are seeking to solve the HSV-1 protease in preparation for 
application of Agouron's drug design technologies. However, no inhibitor of 
HSV-1 or CMV has yet been selected by Agouron for development. 

     Hepatitis C Protease Inhibitors

     The ability to treat infection by hepatitis C virus represents a 
significant unmet clinical need, particularly in Asian countries. Hepatitis 
C virus depends upon a key protease enzyme for the production of new 
infectious viruses. As no human counterpart of the hepatitis C protease 
enzyme is known, Agouron scientists believe that the potential for toxicity 
of selective hepatitis C protease inhibitors is low. Agouron's anti-
hepatitis C project is an early stage research program in which no inhibitor 
has been selected for development. 

Inflammatory Disease

     Overview

     Another scientific and commercial focus of the Company is the 
development of drugs for treatment of inflammatory disease. These include 
MMP inhibitors for use against degenerative diseases such as rheumatoid 
arthritis and osteoarthritis and AICART inhibitors for use as anti-
inflammatory agents and immuno-suppressive agents for treatment of various 
neuro-degenerative disorders. 
<PAGE>
     MMP Inhibitors

     In addition to their role in the growth and metastasis of solid tumors, 
MMPs display high levels of enzymatic activity in such degenerative diseases 
as rheumatoid arthritis and osteoarthritis. Certain members of the MMP 
family are associated most closely with these disease states and, Agouron 
believes, offer targets for orally active drugs with potential for minimal 
toxicity. The development of MMP inhibitors associated with these disease 
states are being pursued by an affiliate of Roche. If successfully developed 
by the Roche affiliate, the Company believes such selective inhibitors of 
certain MMPs have the potential to interrupt the progression of arthritic 
disease itself rather than just to treat the symptoms. The Company will 
receive a royalty on sales by Roche of any anti-inflammatory products 
resulting from the collaborative program. 

     AICART Inhibitors

     AICART is being pursued by Agouron scientists as a target for the 
development of novel anti-inflammatory drugs. It is widely believed that the 
anti-inflammatory effects observed following administration of low doses of 
the anti-cancer drug methotrexate result from the drug's indirect inhibition 
of AICART. Used for chronic therapy, methotrexate accumulates in the liver 
and other tissues and frequently results in serious toxicity. Agouron 
scientists believe that inhibitors of AICART designed to avoid accumulation 
in tissues may be superior anti-inflammatory drugs for conditions such as 
arthritis. The Company's initial lead compounds in this program are being 
used to validate this assertion. Having solved the three-dimensional 
molecular structure of the AICART enzyme, Agouron scientists believe they 
are uniquely positioned to initiate protein structure-based drug design of 
novel inhibitors of the AICART enzyme intended to be efficacious in the 
treatment of inflammatory disease. No candidate for development has yet been 
identified in this program. The Company presently retains all commercial 
rights to any compounds resulting from this program. 

Research and Development Agreements

     The Company has funded its research and development primarily from 
working capital generated from both private and public sales of Agouron 
equity and corporate collaborative arrangements.  The Company has an ongoing 
program of business development which may, from time to time, lead to the 
establishment of corporate collaborations in addition to those noted below. 

     Japan Tobacco Inc. 

     In December 1992, the Company entered into an agreement with JT to 
collaborate on the discovery, development and commercialization of novel 
therapeutic drugs which act on key proteins related to the human immune 
system (JT 1992). In February 1994, the Company expanded its strategic 
alliance with JT into the field of anti-viral drugs for the treatment of 
infections caused by hepatitis C, the herpes family of viruses and 
rhinoviruses (JT 1994). In December 1994, the Company added its anti-HIV 
drug, VIRACEPT, to the JT collaboration with the execution of a worldwide 
development and licensing agreement (JT HIV). In January 1995, JT 1992 was  
canceled by mutual agreement and JT 1992 resources were reallocated to JT 
1994 programs. In February 1996, the portion of the JT 1994 collaboration 
targeting rhinovirus was ended and program resources were reallocated to 
other JT 1994 programs. 

     Under the provisions of JT 1994, JT has agreed to make certain research 
payments of not less than $8,000,000 to the Company over a two-year period 
ending December 1996. Such payments could approximate more than $21,000,000 
over a four-year period if certain technical milestones are achieved. In 
addition, JT made an up-front payment of $7,778,000, which was amortized to 
revenue over a twenty-four month period. Under the provisions of JT HIV, JT 
has made payments of $30,000,000 to Agouron representing initial and 
subsequent payments of $2,500,000, $3,500,000 and $24,000,000.  Agouron and 
JT will ultimately share equally the costs of further development of 
VIRACEPT. 
<PAGE>
     Under the provisions of JT 1994, the Company will have exclusive rights 
to develop, manufacture and market anti-hepatitis C and anti-herpes drugs in 
the United States, Canada and Mexico. JT will have exclusive rights to 
develop, manufacture and market these drugs in Japan, Taiwan and South 
Korea. Outside the countries in which they respectively have exclusive 
rights, Agouron and JT will have co-exclusive rights to manufacture and 
market jointly developed anti-hepatitis C and anti-herpes drugs. Each 
company will pay royalties to the other based upon their respective sales of 
anti-hepatitis C and anti-herpes drugs. Under the provisions of JT HIV, 
Agouron will retain exclusive commercial rights to VIRACEPT (with the right 
to sublicense, subject to JT's right of first refusal) in the United States, 
Canada and Mexico. JT will have exclusive commercial rights to VIRACEPT
(with the right to sublicense, subject to the Company's right of first 
refusal) in Japan and certain other countries of Asia. Exclusive commercial 
rights (with the right to sublicense) in Europe and all remaining countries 
of the world will be held by a joint venture owned equally by Agouron and 
JT. The two companies will share royalties or profits equally from the 
worldwide commercialization of VIRACEPT. 

     Under a separate agreement dated December 1992, JT purchased 155,844 
shares of newly issued Common Stock for an aggregate purchase price of 
$3,000,000. Such purchase represented approximately 2% of the then 
outstanding Common Stock. 

     Roche

     In June 1996, the Company completed a three-year agreement entered into 
with Syntex (U.S.A.) Inc. (now a subsidiary of Roche) to collaborate on the 
discovery of novel matrix metalloprotease inhibitor drugs. Roche has 
exclusive worldwide commercial rights in any MMP inhibitors used to treat 
arthritis and other degenerative bone diseases, subject to the payment of 
royalties to Agouron. Under the terms of the agreement, the Company will 
have a royalty position in certain other agreement products, if any, and 
other development and commercial rights in other agreement products, if any. 

     Under a separate agreement dated June 1993, Syntex Corporation (now a 
subsidiary of Roche) purchased 155,844 shares of newly issued Common Stock 
for an aggregate purchase price of $3,000,000. Such purchase represented 
approximately 2% of the then outstanding Common Stock. 

     In June 1996, Agouron signed a binding letter of intent with Hoffmann-
La Roche Inc. and F. Hoffmann-La Roche Ltd., subsidiaries of Roche, 
providing for the collaborative development and commercialization of 
THYMITAQ and of the Agouron anti-cancer compound designated AG3340 currently 
under preclinical development. Agouron has received initial license fees of 
$15,000,000 and, under the provisions of the binding letter of intent, is to 
receive additional development milestone payments of up to $40,000,000 from 
Roche. Roche has agreed to bear 80% of future costs of developing these 
drugs. Agouron and Roche will cooperatively market the two compounds for
cancer indications and share profits in North America, while Roche has 
exclusive marketing rights for cancer indications to these compounds outside 
North America, subject to possible co-promotion rights and the payment of 
royalties to Agouron. Roche is to provide annual research support of 
$3,000,000 for three years as well as subsequent milestone payments of up to 
$20,000,000 to Agouron for similar commercial rights for all indications in 
compounds which are generated in a collaborative research program focused on 
cell cycle control. Roche also has agreed to grant Agouron the right in 
North America to commercialize a Roche anti-cancer product to be designated 
in the future. 
<PAGE>
     Schering-Plough Corporation

     In April 1994, the Company and Schering completed a three-year 
collaborative research agreement providing for the discovery and development 
of anti-cancer drugs which target oncogenic ras proteins. Each company may 
pursue further discovery or development efforts in this program area at its 
sole discretion and expense with no subsequent obligations to the other 
company. 

Competition

     The pharmaceutical and biotechnology industries are subject to intense 
competition and rapid and significant technological change. Many companies 
and organizations, including major pharmaceutical, biotechnology and 
chemical companies, universities and other research organizations, are 
engaged in discovery and development of drugs for diseases targeted by the 
Company. For example, the Company is aware of several pharmaceutical 
companies that have HIV protease inhibitors, some of which are currently 
being marketed, including those of Abbott Laboratories, Inc., Merck & Co., 
Inc. and Roche. Certain companies and organizations have substantially 
greater financial and other resources, larger research and development 
staffs and more extensive production and marketing organizations, experience 
and capabilities than the Company. In addition, many companies have 
significantly greater experience than the Company in preclinical testing and 
in conducting human clinical trials of potential pharmaceutical products and 
in obtaining the FDA and other regulatory approvals. All of these companies 
and other research organizations compete with the Company in recruiting and 
retaining highly qualified scientific and management personnel. 

     Agouron was the first company to devote itself to the development and 
application of protein structure-based drug design. As such, the Company 
believes that it has achieved certain competitive advantages including 
developmental lead time, level of commitment to the technology and the 
development of certain practical or technical capabilities. However, in 
recent years several pharmaceutical companies have undertaken to establish 
capabilities in protein x-ray crystallography, either internally or through 
academic collaborations, and can be presumed to be engaged in the use of 
such technology for the same purposes as is the Company. Certain 
biotechnology companies and other companies have also entered into the field 
of protein structure-based drug design. For example, Abbott Laboratories, 
Ciba-Geigy Limited, Glaxo Wellcome plc, Merck and Roche have developed 
programs focused on structure-based drug design. The Company expects that 
the technology for protein structure-based drug design will become more 
widely implemented over time and will ultimately become more common in the 
pharmaceutical industry. 

     The Company believes that its ability to compete successfully will be 
based on its ability to create and maintain scientifically advanced 
technology, attract and retain scientific personnel with a broad range of 
expertise, obtain patent protection or otherwise develop proprietary 
products or processes, conduct clinical trials and obtain required 
government approvals on a timely basis, select and pursue drug design 
projects in areas in which significant market opportunities exist or are 
likely to develop, manufacture its products on a cost-effective basis and 
successfully market its products either alone or in conjunction with others. 
Many of the Company's competitors have substantially greater financial 
resources, clinical and regulatory experience, manufacturing capabilities 
and sales and marketing organizations than Agouron. 

Patents and Trade Secrets

     The Company seeks patent protection for its proprietary technology and 
potential products in the United States and in foreign countries. Most of 
the Company's products are expected to be synthetic chemical compounds which 
may be afforded patent protection under principles and procedures well 
established by the United States Patent and Trademark Office under United 
States patent law. 
<PAGE>
     The Company's strategy is to pursue a strong patent portfolio and 
Agouron holds several patents, including a patent covering the chemical 
composition of VIRACEPT. The Company is currently prosecuting a number of 
patent applications in the United States and in various other countries 
seeking protection for certain series of compounds, including, THYMITAQ and 
VIRACEPT and certain proprietary technology. The Company will continue to 
file patent applications on its evolving technology, processes and products. 
The Company has recently received one United States patent covering 
processes of making THYMITAQ and related compounds and intermediates 
thereof. The Company's failure to obtain patent protection for its products 
could have an adverse impact on the Company. 

     Many of the processes and much of the know-how of importance to the 
Company's technology are dependent upon the skills, knowledge and experience 
of its scientific and technical personnel, which skills, knowledge and 
experience are not patentable. To protect its rights in these areas, the 
Company requires all employees, significant consultants and advisors, and 
collaborators to enter into confidentiality agreements with Agouron. There 
can be no assurance, however, that these agreements will provide meaningful 
protection for the Company's trade secrets, know-how or other proprietary 
information in the event of any unauthorized use or disclosure of such trade 
secrets, know-how or proprietary information. Further, in the absence of 
patent protection, the Company may be exposed to competitors who 
independently develop substantially equivalent technology or otherwise gain 
access to the Company's trade secrets, knowledge or other proprietary 
information. 

Government Regulation

     The production and marketing of the Company's products and its ongoing 
research and development activities are subject to regulation for safety, 
efficacy and quality by numerous governmental authorities in the United 
States and other countries. Pharmaceutical products intended for therapeutic 
use in humans are principally governed by the FDA regulations in the United 
States and by comparable government regulations in foreign countries. 
Various federal, state and local statutes and regulations also govern or 
influence the research and development, manufacturing, safety, labeling, 
storage, record keeping, distribution and marketing of such products. The 
process of completing preclinical and clinical testing and obtaining the 
approval of the FDA and similar health authorities in foreign countries to 
market a new drug product requires a significant number of years and the 
expenditure of substantial resources. Failures or delays by the Company or 
its collaborators or licensees in obtaining regulatory approvals would 
adversely affect the marketing of products being developed by the Company 
and the Company's ability to receive product revenues or royalties. 

     The steps required by the FDA before a new human pharmaceutical product 
may be marketed in the United States include: (a) preclinical laboratory 
tests, in vivo preclinical studies and formulation studies; (b) the 
submission to the FDA of a request for authorization to conduct clinical 
trials on an Investigational New Drug Application ("IND"), which must become 
effective before human clinical trials may commence; (c)adequate and well-
controlled human clinical trials to establish the safety and efficacy of the 
drug for its intended use; (d) submission to the FDA of a NDA; and 
(e) review and approval of the NDA by the FDA before the drug product may be 
shipped or sold commercially. Prior to obtaining FDA approval for each 
product, each manufacturing establishment for new drugs must be registered 
with and receive appropriate approval by the FDA. 

     Preclinical tests include laboratory evaluation of product chemistry 
and formulation, as well as animal studies to assess the safety and efficacy 
of the product. Preclinical test results are submitted to the FDA as a part 
of the IND. Clinical trials are typically conducted in three sequential 
phases, although the phases may overlap. Phase I represents the initial 
administration of the drug to a small group of humans, either healthy 
volunteers or patients, to test for safety, dosage tolerance, absorption, 
distribution, metabolism, excretion and clinical pharmacology and, if 
possible, early indications of effectiveness. Phase II involves studies in a 
small sample of the actual intended patient population to assess the 
efficacy of the investigational drug for a specific clinical indication, to 
<PAGE>
ascertain dose tolerance and the optimal dose range and to collect 
additional clinical information relating to safety and potential adverse 
effects. Once an investigational drug is found to have some efficacy and an 
acceptable clinical safety profile in the targeted patient population, phase 
III studies are often initiated to further establish safety and efficacy of 
the investigational drug in a broader sample of the target patient 
population. The results of the clinical trials together with the results of 
the preclinical tests and complete manufacturing information are submitted 
in a NDA to the FDA for approval. 

     If a NDA is submitted to the FDA, there can be no assurance that such 
application will be reviewed and approved by the FDA in a timely manner, if 
at all. Even after initial FDA approval has been obtained, further studies, 
including post-market studies, may be required to provide additional 
information. Results of such post-market programs may limit or expand the 
further marketing of the product. 

     The Company is also subject to foreign regulatory requirements 
governing development, manufacturing and sales of pharmaceutical products 
that vary widely from country to country. Approval of a drug by applicable 
regulatory agencies of foreign countries must be secured prior to the 
marketing of such drug in those countries. The regulatory approval process 
may be more or less rigorous from country to country and the time required 
for approval may be longer or shorter than that required in the United 
States. 

     In addition to the regulatory framework for pharmaceutical product 
approvals, the Company is and may become subject to various federal, state, 
local and foreign laws, regulations and recommendations relating to safe 
working conditions, laboratory and manufacturing practices, the experimental 
use of animals and the use and disposal of hazardous or potentially 
hazardous substances, including radioactive compounds and infectious disease 
agents, used in connection with Agouron's research and development work. The 
Company is unable to predict the extent of restrictions that might arise 
from any governmental or administrative action. 

Manufacturing

     The Company currently has no manufacturing facilities for production of 
commercial quantities of any compounds under development as pharmaceutical 
products. The Company's facilities include scale-up laboratories in which 
the Company intends to produce, under GMP, amounts of its drug product 
candidates sufficient for use in certain early clinical trials. The Company 
is and will be relying upon third parties to manufacture its products in 
quantities sufficient to meet both clinical and commercial needs. The 
Company will be dependent upon these manufacturers to comply with GMP and to 
meet its production requirements. There can be no assurance that these 
manufacturers will timely deliver sufficient quantities of the Company's 
products or that the Company would be able to find substitute manufacturers, 
if necessary. 

Marketing

     The Company does not currently market any pharmaceutical products but 
intends to market any approved cancer and anti-HIV products in North America 
through its own sales and marketing organization. The Company has begun to 
establish its sales and marketing organization by hiring key sales and 
marketing management personnel who possess significant pharmaceutical 
industry experience. Additional sales and marketing personnel will be hired
and certain programs will be implemented upon the achievement of clinical
development milestones, including the successful completion of pivotal 
clinical trials and the submission of a NDA. The Company intends to possess 
the capability to launch products concurrent with their approval by the FDA. 
The Company's sales and marketing efforts will utilize a field sales 
organization focused primarily on office and hospital based physicians 
including key medical thought leaders  Additionally, the Company will seek 
to ensure market access and availability for its products in part by 
establishing relationships within key market segments including health 
maintenance organizations, third-party payers and governmental agencies. 
<PAGE>
Human Resources

     As of June 30, 1996, the Company had 374 employees, 96 of whom hold 
Ph.D. or M.D. degrees. Three hundred employees are engaged in, or directly 
support, research and product development. The Company's employees are not 
covered by a collective bargaining agreement and the Company considers its 
relations with its employees to be excellent. The Company has entered into 
confidentiality agreements with all of its employees. 


Item 2.     PROPERTIES

     The Company leases space in four facilities located in La Jolla, 
California which provide a total of approximately 145,000 square feet of 
office and laboratory space. The Company's corporate headquarters are 
located at 10350 North Torrey Pines Road, La Jolla, California 92037, where 
the Company occupies approximately 36,000 square feet under three leases 
which expire in April 1997.  Additional administrative facilities are 
located at 3301 Torrey Pines Court, La Jolla, California 92037, where the 
Company is the sole tenant and is to occupy approximately 41,300 square feet 
of office space pursuant to a lease expiring August 31, 1999.  Research and 
development activities are conducted at 3565 General Atomics Court, San 
Diego, California 92121 (where the Company is the sole tenant and occupies 
approximately 43,500 square feet under a lease which expires September 2001) 
and at 11099 North Torrey Pines Road, La Jolla, California 92037 (where the 
Company occupies approximately 24,500 square feet under a lease which 
expires in September 2000). These two research and development buildings 
provide state-of-the-art facilities designed specifically to implement and 
support the Company's innovative approach to drug design. Included in the 
facilities are approved scale-up laboratories in which kilogram quantities 
of Company-designed drug compounds are manufactured under current GMP for 
use in clinical trials. Additionally, the Company leases approximately 1,000 
square feet of office space in the United Kingdom which it utilizes for its 
European clinical staff.  The Company is negotiating an additional lease for 
a total of approximately 24,000 square feet to provide additional laboratory 
space. Additional facilities will be necessary if the Company undertakes 
commercial manufacturing. 


Item 3.     LEGAL PROCEEDINGS

     The Company is involved in certain legal proceedings generally 
incidental to its normal business activities.  While the outcome of any such 
proceedings cannot be accurately predicted, the Company does not believe the 
ultimate resolution of any such existing matters should have a material 
adverse effect on its financial position or results of operations. 


Item 4.     SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS

     No matters were submitted during the fourth quarter of the year ended 
June 30, 1996 to a vote of the Company's security holders. 

<PAGE>
                                   PART II


Item 5.     MARKET FOR THE REGISTRANTS' COMMON EQUITY AND RELATED 
            STOCKHOLDER MATTERS

     The Company's common stock is traded in the over-the-counter market and 
prices are quoted on The Nasdaq Stock Market under the symbol AGPH.  The 
following table sets forth the high and low selling prices as reported by 
The Nasdaq Stock Market for the periods indicated. 


1995

     First Quarter                                $  13 3/4     $   9 3/4
     Second Quarter                                  13 1/4        10
     Third Quarter                                   19            10 7/8
     Fourth Quarter                                  27 1/4        15

1996

     First Quarter                                $  39 1/4     $  22 3/4
     Second Quarter                                  35 7/8        22 1/2
     Third Quarter                                   47 5/8        32 3/4
     Fourth Quarter                                  47            32

     On September 13, 1996, the closing price of the Company's common stock 
as reported by The Nasdaq Stock Market was $41.00 per share.  There were 
approximately 10,000 shareholders of the common stock of the Company as of 
such date.  The Company has not paid cash dividends on its common stock and 
does not intend to do so in the foreseeable future. 



Item 6.     SELECTED FINANCIAL DATA

     The following table summarizes certain selected financial data for each 
of the five years in the period ended June 30, 1996.  The information 
presented should be read in conjunction with the financial statements 
included elsewhere in this report. 
<TABLE>
<CAPTION>

(In thousands, except per share amounts) 

                  Years ended 
                  June 30,     1996     1995     1994      1993     1992
                  ----------------------------------------------------------
<S>                           <C>      <C>       <C>      <C>      <C>
Statement of Operations Data: 
     Revenues                 $ 60,731 $ 27,961  $ 17,651 $  9,970 $  6,847
     Net loss                  (19,523) (12,939)   (9,462)  (9,829)  (9,132) 
     Net loss per common share   (1.98)   (1.77)    (1.31)   (1.40)   (1.47) 
     Shares used in computing
       net loss per common share 9,844    7,296     7,241    6,997    6,199

Balance Sheet Data: 
     Working capital          $ 70,381 $  8,837  $ 21,039 $ 29,933 $ 35,115
     Total assets              100,224   27,097    37,178   41,721   45,625
     Long-term liabilities       1,734    1,884     2,285    2,613    3,050
     Stockholders' equity       75,583   12,591    24,852   33,757   37,517
</TABLE>

The Company has never declared or paid dividends on its common stock. 

<PAGE>
Item 7.     MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND 
            RESULTS OF OPERATIONS

Overview

     This discussion contains forward-looking statements and such statements 
are subject to certain risks and uncertainties which could cause actual 
results to differ materially from those projected.  See "Important  Factors 
Regarding Forward-Looking Statements" attached as Exhibit 99 to this annual 
report on Form 10-K.  Readers are cautioned not to place undue reliance on 
these forward-looking statements which speak only as of the date hereof. 
The Company undertakes no obligation to publicly release the result of any 
revisions to these forward-looking statements which may be made to reflect 
events or circumstances after the date hereof or to reflect the occurrence 
of unanticipated events. 

     The Company has been engaged in the research and development of human 
pharmaceuticals utilizing protein structure-based drug design since its 
inception in 1984.  Such research and development has been funded 
principally from the Company's equity-derived working capital and through 
collaborative arrangements with other companies.  The Company's net 
operating losses incurred since inception are primarily a result of the 
Company's independent research and development activities and an increasing 
investment in the clinical development of (and the implementation of a 
commercial infrastructure in support of) its two leading compounds in cancer 
and AIDS.  Net losses for the fiscal years ended June 30, 1996, 1995 and 
1994 were $19,523,000, $12,939,000 and $9,462,000.  It is anticipated that 
net operating losses will continue and will possibly increase through at 
least the next two years. 

Results of Operations

     Collaborative research and development agreements with Japan Tobacco 
Inc. ("JT"), Schering-Plough Corporation ("Schering") and Syntex (U.S.A.) 
Inc., Hoffmann-La Roche Inc. and F. Hoffmann-La Roche Ltd. (collectively 
"Roche") accounted for approximately 99%, 97% and 94% of the Company's total 
contract and license revenues for 1996, 1995 and 1994.  Total contract and 
license revenues for 1996 increased approximately 109% over 1995 due mainly 
to the effect of a full year of increasing program activities on the anti-
HIV collaboration with JT (initiated in December 1994 -- "JT HIV") and the 
initial payments associated with a new (June 1996) collaboration with Roche. 
The increase in contract and license revenues from 1994 to 1995 of 
approximately 64% was due principally to the JT HIV collaboration, the 
effect of a full year of program activities on the anti-viral collaboration 
with JT initiated in February 1994 ("JT 1994") and increased activities for 
research programs with Roche.  These increases were partially offset by the 
absence of funding in 1995 from Schering due to the completion of a 
collaborative research program in April 1994.  The Company anticipates that 
its contract revenues for 1997 will exceed the level of such revenues 
recognized in 1996. 

     Interest income increased from 1995 to 1996 due to a higher average 
balance of cash, cash equivalents and short-term investments resulting from 
the receipt of a $24,000,000 payment from JT in August 1995 and a public 
offering of common stock in September 1995.  Interest income decreased from 
1994 to 1995 primarily due to a generally declining balance of cash, cash 
equivalents and short-term investments which were utilized to fund 
operations.  The Company anticipates that interest income will increase in 
1997. 

     Research and development spending increased by approximately 96% from 
1995 to 1996 and 52% from 1994 to 1995 due generally to increasing average 
research and development staff levels (approximately 23% and 22%) and staff-
related expenditures, including occupancy, and significantly increased 
expenditures for human clinical trial activities associated with the 
Company's leading product candidates: THYMITAQ for the treatment of cancer 
<PAGE>
and VIRACEPT for the treatment of HIV infection and AIDS.  Collaborator-
funded program expenditures representing 72%, 65% and 45% of total research 
and development costs and expenses in 1996, 1995 and 1994, generated a 
significant majority of the increases in research and development costs and 
expenses.  The Company's self-funded research and development programs 
generated approximately 28%, 35% and 55% of total research and development 
costs and expenses in 1996, 1995 and 1994.  Of such self-funded costs during 
1996, 1995 and 1994, approximately 33%, 49% and 44% was dedicated to the 
preclinical and clinical development of the Company's most advanced cancer 
programs.  The Company anticipates that total research and development costs 
and expenses will increase in 1997 in response to expanding preclinical 
activities and clinical studies associated with several of the Company's 
product development programs. 

     General and administrative costs and expenses represented approximately 
11% of total costs and expenses in each of 1996, 1995 and 1994.  Spending 
increases from 1995 to 1996 and 1994 to 1995 are due principally to 
increasing average staff levels (approximately 38% and 36%) and staff-
related expenditures including occupancy.  Also contributing to the 1996 
increase are certain costs associated with a growing sales and marketing 
infrastructure.  The Company anticipates that total general and 
administrative costs and expenses will increase in 1997 due to additional 
staff and occupancy costs and increasing commercial development and sales 
and marketing activities. 

     Interest expense decreased in 1996 due to a decreasing level of debt 
and capital lease obligations but such decrease was totally offset by the 
exercise costs associated with certain lease buy-out options.  Interest 
expense increased by approximately 15% from 1994 to 1995 due to fluctuations 
in interest rates and the level of debt and capital lease obligations from 
year to year. 

Financial Condition

     Liquidity and Capital Resources  

     Since its inception, the Company's cash expenditures have substantially 
exceeded its revenues and the Company has relied primarily on equity, lease 
and debt financing and various collaborative arrangements to fund its 
proceeds of approximately $236,000,000, principally from corporate and 
venture capital investors and through its public offerings in calendar 1987, 
1989, 1991, 1995 and 1996.  The Company believes that its current capital 
resources, existing contractual commitments and the proceeds from a 
secondary public offering in July 1996 (see Note 9) are sufficient to 
maintain its current and planned operations through fiscal 1998.  This 
belief is based on current research and clinical development plans, 
anticipated working capital requirements associated with the planned 
commercial launch of VIRACEPT during fiscal 1997, the current regulatory 
environment, historical industry experience in the development of 
therapeutic drugs and general economic conditions. 

     The Company believes that additional financing may be required to meet 
the planned operating needs of fiscal 1999 if significant positive cash 
flows are not generated from commercial activities.  Such needs would 
include the expenditure of substantial funds to continue research and 
development activities, conduct existing and planned preclinical studies and 
tests, conduct human clinical trials and to support a growing commercial 
infrastructure, including certain manufacturing, sales and marketing 
capabilities.  As a result, the Company anticipates pursuing various 
financing alternatives such as collaborative arrangements and additional 
public offerings or private placements of Company securities.  If such 
alternatives are not available, the Company may be required to delay or 
eliminate expenditures for certain of its potential products under 
development or to license third parties to commercialize products or 
technologies that the Company would otherwise seek to develop or 
commercialize itself. 
<PAGE>
     Capital Expenditures

     During 1996, capital expenditures totaled $3,710,000 compared with 
$2,032,000 and $1,829,000 during 1995 and 1994, of which $457,000, $17,000 
and $58,000 were financed through capital lease obligations.  Of the total 
capital expenditures during 1996, 1995 and 1994, approximately $318,000, 
$130,000 and $119,000 represented leasehold improvement costs associated 
with certain of the Company's facilities.  With the exception of the 
leasehold improvement costs, virtually all of the capital expenditures 
during 1996, 1995 and 1994 represented laboratory and office equipment and 
scientific instrumentation necessary to support an expanding research, 
development, and commercial infrastructure. 

     Capital expenditures during 1997 are expected to be approximately 
$3,300,000 to support product commercialization, development and research 
activities.  The Company may utilize lease or debt financing for certain 
expenditures if available on acceptable terms. 

     New Accounting Pronouncement

     In October 1995, the Financial Accounting Standards Board issued 
Statement of Financial Accounting Standards No. 123 "Accounting for Stock-
Based Compensation" ("FAS 123").  This Statement defines a fair value method 
of accounting for an employee stock option or similar equity instrument and 
encourages adoption of that method.  Under FAS 123, an employer's financial 
statements should include certain disclosures about stock-based compensation 
arrangements regardless of the method used to account for them.  The 
Statement is effective for financial statements for fiscal years that begin 
after December 15, 1995.  As permitted by FAS 123, the Company will continue 
to follow the existing accounting requirements for stock options and stock-
based awards contained in APB Opinion No. 25 ("Accounting for Stock Issued 
to Employees").  However, beginning in fiscal 1997, the Company will provide 
the pro-forma disclosures required by FAS 123 for entities electing not to 
adopt the fair value accounting method specified in FAS 123.  The adoption 
of FAS 123 in fiscal 1997 will have no material impact on liquidity or 
capital resources. 

<PAGE>
Item 8.     FINANCIAL STATEMENTS AND SUPPLEMENTARY DATA

INDEX TO FINANCIAL STATEMENTS AND SCHEDULES                            PAGE

Report of Independent Accountants                                      F-1

Balance Sheet as of June 30, 1996 and 1995                             F-2

Statement of Operations for the years ended                            F-3
     June 30, 1996, 1995 and 1994

Statement of Stockholders' Equity for the                              F-4
     years ended June 30, 1996, 1995 and 1994

Statement of Cash Flows for the years ended                            F-5
     June 30, 1996, 1995 and 1994 

Notes to Financial Statements                                          F-6

     NOTE:     All schedules are omitted because they are either not 
               applicable or not required or the information is shown 
               elsewhere in the financial statements or in the notes 
               thereto. 

PAGE>
                         REPORT OF INDEPENDENT ACCOUNTANTS


To the Board of Directors and Stockholders of Agouron Pharmaceuticals, Inc. 

In our opinion, the accompanying balance sheet and the related statements of 
operations, of stockholders' equity and of cash flows present fairly, in all 
material respects, the financial position of Agouron Pharmaceuticals, Inc. 
at June 30, 1996 and 1995, and the results of its operations and its cash 
flows for each of the three years in the period ended June 30, 1996, in 
conformity with generally accepted accounting principles.  These financial 
statements are the responsibility of the Company's management; our 
responsibility is to express an opinion on these financial statements based 
on our audits.  We conducted our audits of these statements in accordance 
with generally accepted auditing standards which require that we plan and 
perform the audit to obtain reasonable assurance about whether the financial 
statements are free of material misstatement.  An audit includes examining, 
on a test basis, evidence supporting the amounts and disclosures in the 
financial statements, assessing the accounting principles used and 
significant estimates made by management, and evaluating the overall 
financial statement presentation.  We believe that our audits provide a 
reasonable basis for the opinion expressed above. 




/s/ PRICE WATERHOUSE LLP

San Diego, California
August 7, 1996













                                   F-1

PAGE>
                          AGOURON PHARMACEUTICALS, INC. 

                                  BALANCE SHEET
                             (Dollars in thousands) 


                                      ASSETS
<TABLE>
<CAPTION>

                                                             June 30, 
Current assets:                                         1996         1995     
                                                     ----------   ----------
<S>                                                  <C>          <C>
     Cash and cash equivalents                       $  16,451    $   4,358
     Short-term investments                             74,424       15,886
     Accounts receivable                                   613          344
     Other current assets                                1,800          871
                                                     ----------   ----------
     Total current assets                               93,288        1,459

Property and equipment, net                              6,936        5,638
                                                      ---------   ----------
                                                     $ 100,224    $   7,097
                                                     ==========   ==========


LIABILITIES AND STOCKHOLDERS' EQUITY


Current liabilities: 

     Accounts payable                                $  10,177    $   5,426
     Accrued liabilities                                   809          683
     Deferred revenue                                   11,435        5,745
     Current portion of long-term debt                     486          768
                                                     ----------   ----------
     Total current liabilities                          22,907       12,622
                                                     ----------   ----------

Long-term liabilities: 

     Long-term debt, less current portion                  501          580
     Accrued rent                                        1,233        1,304
                                                     ----------   ----------
     Total long-term liabilities                         1,734        1,884
                                                     ----------   ----------

Stockholders' equity: 

     Common stock, no par value, 75,000,000 shares
        authorized, 10,731,687 and 7,359,282 shares
        issued and outstanding                         158,628       76,113
     Accumulated deficit                               (83,045)     (63,522) 
                                                     ----------   ----------
     Total stockholders' equity                         75,583       12,591
                                                     ----------   ----------
Commitments (Note 8)                                      --            --   
                                                     ----------   ----------
                                                     $ 100,224    $  27,097
                                                     ==========   ==========
</TABLE>

                  See accompanying notes to financial statements. 

                                        F-2
<PAGE>

                            AGOURON PHARMACEUTICALS, INC. 

                              STATEMENT OF OPERATIONS
                      (In thousands, except per share amounts) 
<TABLE>
<CAPTION>


                                                  Year ended June 30, 
                                          ----------------------------------
                                             1996        1995        1994     
                                          ----------  ----------  ----------
<S>                                       <C>         <C>         <C>

Revenues: 
     Contract and license                 $  55,955   $  26,722   $  16,301
     Interest                                 4,776       1,239       1,350
                                          ----------  ----------  ----------
                                             60,731      27,961      17,651
                                          ----------  ----------  ----------
Costs and expenses: 
     Research and development                71,010      36,317      23,957
     General and administrative               9,016       4,358       2,961
     Interest                                   228         225         195
                                          ----------  ----------  ----------
                                             80,254      40,900      27,113
                                          ----------  ----------  ----------
Net loss                                  $ (19,523)  $ (12,939)  $  (9,462) 
                                          ==========  ==========  ==========
Net loss per common share                 $   (1.98)  $   (1.77)  $   (1.31) 
                                          ==========  ==========  ==========
Shares used in computing net loss
   per common share                           9,844       7,296       7,241
                                          ==========  ==========  ==========
</TABLE>

                See accompanying notes to financial statements. 








                                        F-3
<PAGE>
                          AGOURON PHARMACEUTICALS, INC. 

                       STATEMENT OF STOCKHOLDERS' EQUITY
                              (Dollars in thousands) 
<TABLE>
<CAPTION>


                                   Common Stock             Accumulated
                                -------------------   ----------------------
                                  Shares     Amount     Deficit      Total
                                ----------  --------   ----------  ---------
<S>                              <C>        <C>        <C>         <C>
Balance at June 30, 1993         7,226,546  $ 74,878   $ (41,121)  $ 33,757

Stock issuances:  
   Exercise of stock options        32,649       352       --           352
   Employee stock purchase plan     19,293       170       --           170
   Options granted for services
   provided                           --          35       --            35
Net loss                              --        --        (9,462)    (9,462) 
                                ----------  ---------  ----------  ---------
Balance at June 30, 1994         7,278,488    75,435     (50,583)    24,852

Stock issuances: 
   Exercise of stock options        49,125       382        --          382
   Employee stock purchase plan     31,669       296        --          296
Net loss                              --        --       (12,939)   (12,939) 
                                ----------  ---------  ----------  ---------
Balance at June 30, 1995         7,359,282    76,113     (63,522)    12,591

Stock issuances: 
   Public sale                   3,000,000    78,579       --        78,579
   Exercise of stock options       293,206     2,990       --         2,990
   Exercise of stock warrants       45,000       283       --           283
   Employee stock purchase plan     34,199       663       --           663
Net loss                              --        --       (19,523)   (19,523) 
                                ----------  ---------  ----------  ---------
Balance at June 30, 1996        10,731,687  $158,628   $ (83,045)  $ 75,583
                                ==========  =========  ==========  =========
</TABLE>

               See accompanying notes to financial statements. 








                                          F-4

<PAGE>
                           AGOURON PHARMACEUTICALS, INC. 

                             STATEMENT OF CASH FLOWS
                              (Dollars in thousands) 

<TABLE>
<CAPTION>
                                                    Year ended June 30, 
                                            --------------------------------
                                               1996       1995       1994     
                                            ---------- ---------- ----------
<S>                                         <C>        <C>        <C>
Cash flows from operating activities: 
   Cash received from contracts and 
     licenses                               $  61,376  $  25,633  $  20,307
   Cash paid to suppliers, employees 
     and service providers                    (73,738)   (34,113)   (24,955) 
   Interest received                            4,776      1,239      1,350
   Interest paid                                 (228)      (225)      (195) 

   Net cash provided (used) by operating 
     activities                                (7,814)    (7,466)    (3,493) 
                                            ---------- ---------- ----------
Cash flows from investing activities: 
   Net (increase) decrease in short-term 
     investments                              (58,538)    11,871       (840) 
   Expenditures for property and equipment     (3,252)    (1,978)    (1,783) 
                                            ---------- ---------- ----------
   Net cash provided (used) by investing 
     activities                               (61,790)     9,893     (2,623) 
                                            ---------- ---------- ----------
Cash flows from financing activities: 
   Net proceeds from issuance of common stock  82,515        678        522
   Principal payments under equipment leases     (373)      (613)      (550) 
   Increase (decrease) in long-term debt, net    (445)      (238)       465
                                            ---------- ---------- ----------
   Net cash provided (used) by financing 
     activities                                81,697       (173)       437
                                            ---------- ---------- ----------
Net increase (decrease) in cash and 
   cash equivalents                            12,093      2,254     (5,679) 
Cash and cash equivalents at beginning
   of year                                      4,358      2,104      7,783
                                            ---------- ---------- ----------
Cash and cash equivalents at end of year    $  16,451  $   4,358  $   2,104
                                            ========== ========== ==========
Reconciliation of net loss to net cash 
   provided (used) by operating activities: 
   Net loss                                 $ (19,523) $ (12,939) $  (9,462)
   Depreciation and amortization                2,411      2,455      2,180
   Net (increase) decrease in accounts 
     receivable and other current assets       (1,198)         4       (635) 
   Net increase (decrease) in accounts 
      payable, accrued liabilities, 
      deferred revenue and other liabilities   10,496      3,014      4,389
   Options granted for services provided         --         --           35
                                            ---------- ---------- ----------
Net cash provided (used) by operating 
   activities                               $  (7,814) $  (7,466) $  (3,493) 
                                            ========== ========== ==========
</TABLE>
                See accompanying notes to financial statements. 









                                          F-5

<PAGE>
                        AGOURON PHARMACEUTICALS, INC. 

                        NOTES TO FINANCIAL STATEMENTS


Note 1 - The Company and its significant accounting policies

     The Company

     Agouron Pharmaceuticals, Inc. ("Agouron" or the "Company") was 
incorporated in the state of California on June 22, 1984 and is engaged in 
the development of human pharmaceuticals utilizing protein structure-based 
drug design. 

     Estimates

     The preparation of financial statements in conformity with generally 
accepted accounting principles requires management to make estimates and 
assumptions that affect the reported amounts of assets, liabilities, 
revenues and expenses and related disclosures as of the date of the 
financial statements.  Actual results could differ from such estimates. 

     At June 30, 1996, it has been assumed that the existing collaborations 
with Japan Tobacco Inc. ("JT") will continue in accordance with their 
agreement terms.  As such, approximately $11,435,000 of cash received from 
JT has been classified as deferred contract revenue, is non-refundable and 
is being recognized as revenue on a prospective basis as collaborative 
program expenses are incurred.  Should any of the underlying collaborations 
be terminated in advance of their contract terms, any deferred contract 
revenues related to such collaborations would immediately be recognized as 
revenue by the Company. 

     Short-term investments

     Short-term investments consist principally of government or government 
agency securities, corporate notes and bonds, commercial paper and 
certificates of deposit with original maturities of three to thirty-six 
months. The Company has classified its short-term investments as available-
for-sale.  Included in short-term investments at June 30, 1996, 1995 and 
1994 is $1,156,000, $172,000 and $246,000 of accrued interest receivable. 

     Concentration of credit and market risk and off balance sheet risk

     The Company invests its excess cash principally in marketable 
securities from a diversified portfolio of institutions with strong credit 
ratings and, by policy, limits the amount of credit exposure at any one 
institution.  These investments are generally not collateralized and 
primarily mature within one year.  The Company has not realized any material 
losses from such investments in 1996, 1995 or 1994. 

     Property and equipment

     Property and equipment is recorded at cost.  Depreciation is computed 
using the straight-line method over estimated useful lives of three to five 
years.  Leasehold improvements are amortized over the life of the lease. 
Charges to costs and expenses for repairs and maintenance were $580,000, 
$422,000 and $534,000 for the years ended June 30, 1996, 1995 and 1994. 



                                          F-6
<PAGE>
     Revenue recognition

     Contract revenues are earned and recognized according to the provisions 
of each collaborative agreement on a percentage-of-completion basis. 
Amounts received in advance of performance are recorded as deferred revenue. 
Contract milestone payments are recognized as revenues upon the completion 
of the milestone event or requirement.  Initial license fee payments are 
recognized as revenue when earned. 

     Statement of cash flows

     For purposes of the Statement of Cash Flows, cash equivalents are 
highly liquid investments purchased with an original maturity of three 
months or less.  Non-cash financing activities are comprised primarily of 
capital lease obligations and were $457,000, $17,000 and $58,000 for 1996, 
1995 and 1994. 

     Income taxes

     The Company recognizes deferred taxes using the liability method, 
whereby tax rates are applied to cumulative temporary differences based on 
when and how they are expected to affect the tax return. 


Note 2 -  Short-term investments

     At June 30, 1996, the amortized cost and estimated fair value of short-
term investments held as available-for-sale were as follows: 


<TABLE>
<CAPTION>
   (Dollars in thousands)     Amortized  Unrealized  Unrealized     Fair
                                 Cost       Gains      Losses       Value
                              ---------  ----------  ----------  ---------
<S>                           <C>        <C>        <C>         <C>
   United States government
      securities              $  62,883  $      25  $     (111)  $  62,797
   Corporate obligations          8,535          2          (1)      8,536
   Other interest bearing 
      securities                  3,006       --         --          3,006
                              ---------  ---------  -----------  ---------
                              $  74,424  $      27  $     (112)  $  74,339
                              =========  =========  ===========  =========
</TABLE>

     Realized gains on the disposal of available-for-sale securities during 
1996 totaled $22,000. During 1995 such gains and losses totaled $3,000 and 
$7,000, respectively.  The cost of securities sold is based upon the 
specific identification method.  At June 30, 1996, scheduled maturities for 
available-for-sale securities were less than twelve months for $69,414,000 
and between twelve and twenty-one months for $5,010,000. 




                                          F-7


<PAGE>
Note 3 - Composition of certain financial statement captions
<TABLE>
<CAPTION>


                                                            June 30, 
                                                   ----------------------
                                                      1996         1995     
                                                   ----------  ----------
                                                   (Dollars in thousands) 
<S>                                                <C>         <C>
Accounts receivable: 
   Employee receivables                            $     211   $     262
   Other receivables                                     402          82
                                                   ----------  ----------
                                                   $     613   $     344
                                                   ==========  ==========
Property and equipment, net: 
   Scientific instrumentation                      $   9,353   $   7,787
   Computer equipment                                  6,881       5,453
   Leasehold improvements                              3,184       2,798
   Furniture and fixtures                              1,228         944
                                                   ----------  ----------
                                                      20,646      16,982
   Less accumulated depreciation and amortization    (13,710)    (11,344) 
                                                   ----------  ----------
                                                   $   6,936   $   5,638
                                                   ==========  ==========
Accrued liabilities: 
   Accrued vacation                                $     735   $     623
   Other                                                  74          60
                                                   ----------  ----------
                                                   $     809   $     683
                                                   ==========  ==========
</TABLE>

Note 4 - Significant contract arrangements

     Roche

     In June 1996, Agouron signed a binding letter of intent (LOI) with 
Hoffmann-La Roche Inc. and F. Hoffmann-La Roche Ltd. (subsidiaries of Roche 
Holdings, Inc. -- "Roche") providing for the worldwide development of two 
anti-cancer drugs currently being developed by the Company and to 
collaborate on an additional early-stage anti-cancer drug discovery program. 
Under the terms of the LOI, in return for rights to the Company's most 
advanced anti-cancer drug (THYMITAQ) and a preclinical anti-cancer compound 
(AG3340), Roche has paid $15,000,000 in initial license fees and has agreed 
to pay milestone payments of up to $40,000,000 and to bear 80% of the future 
development costs of these two drugs.  In North America, the Company and 
Roche will cooperatively market the two drugs and will share equally in 
resulting profits.  Outside of North America, Roche will lead 
commercialization efforts and pay royalties to the Company or, in certain 
circumstances, will share profits with the Company.  For similar commercial 
rights to compounds generated in a collaborative research program focused on 
cell cycle control (initially targeting the enzyme cdk4), Roche is to 
provide annual research support to the Company of $3,000,000 as well as 
subsequent milestone payments of up to $20,000,000 and has agreed to bear 
80% of any post-research development costs.  The Company also has a right in 
North America to commercialize a Roche anti-cancer product to be named in 
the future.  Under the LOI, the Company received and recognized as revenue, 
the initial license payment of $15,000,000. 


     In June 1996, the Company completed a three-year agreement with Syntex 
(U.S.A.) Inc. (now a subsidiary of Roche), to collaborate on the discovery 
of novel matrix metalloprotease inhibitor drugs.  Each company may pursue 
further discovery or development efforts in this program area at its sole 
discretion and expense with no subsequent obligations to the other company. 

                                          F-8
<PAGE>
Under the agreement, the Company incurred costs and recognized corresponding 
revenues of $3,013,000, $3,043,000 and $2,307,000 during the years ended 
June 30, 1996, 1995 and 1994.  The Company funded a portion of the 
activities associated with this collaboration on its own account. 

     Under a separate agreement dated June 1993, Roche purchased 155,844 
shares of newly issued common stock of the Company for an aggregate purchase 
price of $3,000,000.  Such purchase represented approximately 2% of the then 
outstanding common stock of the Company. 

     Japan Tobacco Inc. 

     In December 1992, the Company entered into an agreement with Japan 
Tobacco Inc. ("JT") to collaborate on the discovery, development and 
commercialization of novel therapeutic drugs which act on key proteins 
related to the human immune system ("JT 1992").  In February 1994, the 
Company expanded its strategic alliance with JT into the field of anti-viral 
drugs for the treatment of infections caused by hepatitis C, the herpes 
family of viruses and the rhinoviruses ("JT 1994").  In December 1994, the 
Company added its anti-HIV drug, VIRACEPT, to the JT collaboration with the 
execution of a worldwide development and licensing agreement ("JT HIV").  In 
January 1995, JT 1992 was canceled by mutual agreement and JT 1992 resources 
were reallocated to JT 1994 programs.  In February 1996, JT 1994 was 
modified to delete rhinoviruses from the strategic alliance. 

     Under the provisions of JT 1994, JT has agreed to make certain research 
payments to the Company of not less than $8,000,000 over a two year period 
ending December 1996.  Such payments could approximate more than $21,000,000 
over a four year period if certain technical milestones are achieved.  In 
addition, JT made an up-front payment of $7,778,000, which was amortized to 
revenue over a twenty-four month period.  Under the provisions of JT HIV, JT 
has made payments of $30,000,000 to Agouron representing initial and 
subsequent payments of $2,500,000, $3,500,000 and $24,000,000.  Additional 
payments representing JT's share of VIRACEPT development costs have also 
been received.  Agouron and JT will ultimately share equally the costs of 
further development of VIRACEPT. 

     Under the provisions of JT 1994, the Company will have exclusive rights 
to develop, manufacture and market anti-hepatitis C and anti-herpes drugs in 
the United States, Canada and Mexico.  JT will have exclusive rights to 
develop, manufacture and market these drugs in Japan, Taiwan and South 
Korea.  Outside the countries in which they respectively have exclusive 
rights, Agouron and JT will have co-exclusive rights to manufacture and 
market jointly developed anti-hepatitis C and anti-herpes drugs.  Each 
company will pay royalties to the other based upon their respective sales of 
anti-hepatitis C and anti-herpes drugs.  Under the provisions of JT HIV, 
Agouron will retain exclusive commercial rights to VIRACEPT (with the right 
to sublicense, subject to JT's right of first refusal) in the United States, 
Canada and Mexico.  JT will have exclusive commercial rights to VIRACEPT
(with the right to sublicense, subject to Agouron's right of first refusal) 
in Japan and certain other countries in Asia.  Exclusive commercial rights 
(with the right to sublicense) in Europe and all remaining countries in the 
world will be held by a joint venture owned equally by Agouron and JT.  The 
two companies will share profits equally from the worldwide 
commercialization of VIRACEPT. 

     Under the combined terms of the agreements, the Company has incurred 
costs of $46,969,000, $19,211,000 and $5,043,000 and recognized 
corresponding revenues of $37,197,000, $22,881,000 and $11,144,000 for the 
years ended June 30, 1996, 1995 and 1994. 

     Under a separate agreement dated December 1992, JT purchased 155,844 
shares of newly issued common stock of the Company for an aggregate purchase 
price of $3,000,000.  Such purchase represented approximately 2% of the then 
outstanding common stock of the Company. 

                                          F-9
<PAGE>
     Schering-Plough Corporation

     In April 1994, the Company and Schering-Plough Corporation ("Schering")
completed a three year collaborative research agreement providing for the 
discovery and development of anti-cancer drugs which target oncogenic ras 
proteins.  Each company may pursue further discovery or development efforts 
in this program area at its sole discretion and expense with no subsequent 
obligations to the other company.  Under the agreement, the Company has 
incurred costs and recognized corresponding revenues of $1,894,000 during 
the year ended June 30, 1994. 


Note 5 - Long-term debt

     Long-term debt and capital lease obligations are as follows: 
<TABLE>
<CAPTION>

                                                           June 30, 
                                                   ----------------------
                                                      1996        1995     
                                                   ----------  ----------
                                                   (Dollars in Thousands) 
<S>                                                <C>         <C>
Notes payable, secured with personal property
   and a certificate of deposit; interest
   at CD rate plus 1.5%, maturing June 1997 
   and November 1998                               $     486   $     931

Capital leases with interest rates between 7.1% 
   and 16.5%, maturing at various dates through 
   December 2000                                         501         417
                                                   ----------  ----------
Total long-term debt and capital lease obligations       987       1,348

Current portion of long-term debt                       (486)       (768) 
                                                   ----------  ----------
Long-term debt                                     $     501   $     580
                                                   ==========  ==========
</TABLE>

     Maturities of long-term debt, excluding capital leases, are as follows: 
1997 - $344,000, 1998 - $100,000, 1999 - $42,000 and 2000 and thereafter $0. 











                                          F-10
<PAGE>
Note 6 - Income taxes

     The Company has deferred income taxes which have been fully reserved as
   follows: 
<TABLE>
<CAPTION>


                                                            June 30, 
                                                  --------------------------
                                                      1996          1995     
                                                  ------------  ------------
                                                     (Dollars in thousands) 
<S>                                               <C>           <C> 

   Deferred revenue                               $     4,694   $     2,358
   Book and tax depreciation differences                2,117         1,664
   Accrued liabilities                                    807           790
   Net operating loss carryforwards                    26,593        19,638
   Foreign tax credits                                  3,746         1,913
   Research and development tax credits                 4,492         3,936
                                                  ------------  ------------
                                                       42,449        30,299
   Valuation allowance                                (42,449)      (30,299) 
                                                  ------------  ------------
   Deferred taxes, net                            $      --     $      --     
                                                  ============  ============
</TABLE>


     The Company has not recorded provisions for any United States income 
taxes due to net operating losses for tax reporting purposes.  At June 30, 
1996, the Company had net operating loss carryforwards for federal tax 
reporting purposes of approximately $72,428,000, expiring from 2000 through 
2011.  The Company also has federal research and development credit 
carryforwards of approximately $2,657,000 at June 30, 1996.  The future 
utilization of, or limitation as to the use of, net operating loss 
carryforwards for federal and state income tax purposes may be impacted by 
the issuance of additional equity securities. 

     As a result of California's partial conformity with federal provisions 
regarding net operating loss and research and development credit 
carryforwards, the Company has net operating loss and research and 
development credit carryforwards of approximately $20,179,000 and $1,731,000 
for state tax reporting purposes at June 30, 1996, expiring from 1997 
through 2001. 

     Included in General and Administrative costs and expenses at June 30, 
1996, 1995 and 1994 is approximately $934,000, $863,000 and $611,000 of 
foreign tax expense associated with the contract research payments from JT. 





                                          F-11
<PAGE>

Note 7 -  Stockholders' equity

     Stock Options

     The Company has two stock option plans whereby 4,220,000 shares of the 
Company's common stock have been reserved for issuance to its officers, 
directors, employees and consultants.  The plans, as amended, are 
administered by the Board of Directors or its designees and provide 
generally that, for incentive stock options, the exercise price shall not be 
less than the fair market value of the shares at the date of grant and, for 
certain non-qualified stock options, the price shall not be less than 85% of 
the fair market value of the shares at the date of grant and may be at any 
price determined by the Board of Directors for others.  The options expire 
not later than ten years from the date of the grant and generally become 
exercisable ratably over a four year period beginning one year from the 
grant date.  At June 30, 1996, 586,842 of these options have been exercised, 
1,330,965 were exercisable and 218,801 shares of common stock remain 
available for grant.  The following table summarizes stock option activity 
for 1994 through 1996: 
<TABLE>
<CAPTION>


                                                Shares           Price     
                                              ----------   -----------------
<S>                                           <C>          <C>
     Outstanding June 30, 1993                1,274,467  
   
     Options granted                            703,450    $  8.63 - $ 16.00
     Options exercised                          (32,649)   $  5.40 - $ 12.00
     Options canceled                           (39,829)   $  7.88 - $ 15.50
                                              ----------
     Outstanding June 30, 1994                1,905,439

     Options granted                            773,275    $ 10.13 - $ 24.50
     Options exercised                          (49,125)   $  5.40 - $ 15.50
     Options canceled                           (43,897)   $  7.88 - $ 16.13
                                              ----------
     Outstanding June 30, 1995                2,585,692

     Options granted                          1,162,475    $ 23.56 - $ 46.00
     Options exercised                         (293,206)   $  5.40 - $ 18.38
     Options canceled                           (40,604)   $  7.88 - $ 39.13
                                              ----------
     Outstanding June 30, 1996                3,414,357
                                              ==========
</TABLE>


     Employee Stock Purchase Plan

     The Company has a stock purchase plan in which eligible employees may 
purchase shares of the Company's common stock through payroll deductions. A 
total of 250,000 shares of common stock have been reserved for issuance 
under the plan, of which 156,414 shares remain available for purchase at 
June 30, 1996.  Funds deducted from participating employees' salaries are 
used to purchase common stock at prices equal to 85% of the fair market 
value of the common stock on either the first or last day of a purchase 
period.  During 1996, 6,131 shares were issued at a price of $9.88 per 
share, 23,240 shares were issued at a price of $19.98 per share and 4,828 
shares were issued at a price of $28.58 per share.  During 1995, 25,524 
shares were issued at a price of $9.24 per share and 6,145 shares were 
issued at a price of $9.88 per share.  During 1994, 10,073 shares were 
issued at a price of $8.29 per share and 9,220 shares were issued at a price 
of $9.35 per share. 






                                          F-12
<PAGE>
Note 8 - Commitments

     Certain scientific instrumentation, computer and other equipment are 
subject to leases which are classified as capital leases.  At June 30, 1996 
and 1995, $897,000 ($484,000, net) and $2,364,000 ($227,000, net) of such 
leased equipment are included in property and equipment. 

     Rental expenses (principally for leased facilities under long-term 
operating lease commitments) were $2,548,000, $2,198,000 and $1,973,000 for 
1996, 1995 and 1994.  Future minimum payments for capital and operating 
leases at June 30, 1996 are as follows (dollars in thousands): 


                                         Capital Leases     Operating Leases
                                         ---------------    ----------------

     1997                                $          148     $         2,793
     1998                                           128               2,266
     1999                                           100               2,313
     2000                                            91               2,411
     2001                                            41               1,872
     Thereafter                                    --                   419
                                         ---------------    ----------------
     Total minimum lease payments                   508     $        12,074
     Less amount representing interest               (7)    ================
                                         ---------------
     Obligation under capital leases     $          501
                                         ===============


     The Company is involved in certain legal proceedings generally 
incidental to its normal business activities.  While the outcome of any such 
proceedings cannot be accurately predicted, the Company does not believe the 
ultimate resolution of any such existing matters should have a material 
adverse effect on its financial position or results of operations. 


Note 9 - Subsequent event

     Subsequent to the end of fiscal 1996, the Company concluded a public 
offering of 2,735,000 shares of its common stock at $30.00 per share which 
generated net proceeds, before offering expenses, of approximately 
$77,537,000. 











                                          F-13
<PAGE>
Item 9.     CHANGES IN AND DISAGREEMENTS WITH ACCOUNTANTS ON ACCOUNTING AND 
            FINANCIAL DISCLOSURE

     None. 
<PAGE>
                                     PART III


Item 10.     DIRECTORS AND EXECUTIVE OFFICERS OF THE REGISTRANT

     The executive officers and directors of the Company are as follows: 


               Name                   Age              Position
     ------------------------------   ---   ---------------------------------
     Peter Johnson                     51     President, Chief Executive 
                                                 Officer and Director

     Neil J. Clendeninn, M.D., Ph.D.   47     Vice President, Clinical 
                                                 Affairs

     Steven S. Cowell                  47     Vice President, Finance and 
                                                 Chief Financial Officer

     Gary E. Friedman                  49     Vice President, General 
                                                 Counsel, Secretary and 
                                                 Director

     Robert C. Jackson, Ph.D.          53     Vice President, Research and 
                                                 Development

     Barry D. Quart, Pharm.D.          39     Vice President, Regulatory 
                                                 Affairs

     R. Kent Snyder                    42     Vice President, Commercial 
                                                 Affairs

     Glenn R. Zinser                   53     Vice President, Operations

     John N. Abelson, Ph.D.(1)         57     Director

     Patricia M. Cloherty(2)           54     Director

     A.E. Cohen(1)                     60     Director

     Michael E. Herman(1)              55     Director

     Irving S. Johnson, Ph.D.          71     Director

     Antonie T. Knoppers, M.D.(2)      81     Director

     Melvin I. Simon, Ph.D.(2)         59     Director

- ----------
(1)      Member of Directors Compensation Committee
(2)      Member of Audit Committee

<PAGE>

     Peter Johnson, a founder of the Company, has served as a director and 
as president and chief executive officer of the Company since its inception 
in 1984.  Through 1989, Mr. Johnson held various positions with The Agouron 
Institute, including executive director.  Mr. Johnson received a M.A. from 
the University of California, San Diego. 

     Neil J. Clendeninn joined the Company in February 1993 as vice 
president, clinical affairs.  From 1985 until joining the Company, Dr. 
Clendeninn held various positions with Burroughs Wellcome Co., including 
head of the chemotherapy section from 1988.  From 1981 through 1985, Dr. 
Clendeninn worked with the clinical oncology and clinical pharmacology 
groups at the National Institutes of Health.  Dr. Clendeninn received a M.D. 
and a Ph.D. in pharmacology from New York University. 

     Steven S. Cowell joined the Company in August 1991 as vice president, 
finance and chief financial officer.  From 1982 until joining the Company, 
Mr. Cowell held various positions, the most recent of which was vice 
president and controller at Cetus Corporation, a public biotechnology 
company primarily engaged in the development, manufacture and marketing of 
pharmaceutical products.  Mr. Cowell is a Certified Public Accountant in 
California and received a B.S. in business administration from the 
University of California, Berkeley. 

     Gary E. Friedman, a founder of the Company, has served as a director 
since its inception, as the secretary of the Company since May 1986 and as 
vice president and general counsel since December 1991.  Previously, from 
1982 until December 1991, Mr. Friedman was a principal of the law firm of 
Friedman, Jay & Cramer, a Professional Corporation.  Mr. Friedman is a 
California Certified Specialist in Taxation.  Mr. Friedman received a 
J.D. and a M.B.A. from the University of California, Berkeley and a L.L.M. 
in taxation from the University of San Diego. 

     Robert C. Jackson joined the Company in March 1991 as vice president, 
research and development.  From June 1990 to February 1991, Dr. Jackson was 
group director of the anti-cancer drug discovery program at The DuPont Merck 
Pharmaceutical Company and, from 1982 to June 1990, held various positions 
with the Parke-Davis Pharmaceutical Research Division of the Warner-Lambert 
Company, including director of tumor biology and director of the 
chemotherapy department.  Dr. Jackson received a Ph.D. in biochemistry from 
the University of London. 

     Barry D. Quart joined the Company in June 1993 as vice president, 
regulatory affairs.  From 1983 until joining the Company, Dr. Quart held 
various positions with Bristol-Myers Squibb Company, including executive 
director of international regulatory affairs from 1992.  Dr. Quart received 
a Pharm.D. in clinical pharmacy from the University of California, San 
Francisco. 

     R. Kent Snyder joined the Company in July 1991 as vice president, 
business development.  In June 1995, Mr. Snyder's title was changed to vice 
president, commercial affairs.  From 1982 until joining the Company, Mr. 
Snyder held various positions with Marion Laboratories, Inc. (now Hoechst 
Marion Roussel), including director of U.S./European licensing.  Prior to 
his employment at Marion, from 1978 to 1982, he held various sales and 
marketing positions with Hoffmann-La Roche Ltd. Mr. Snyder received a M.B.A. 
from Rockhurst College. 

     Glenn R. Zinser joined the Company in 1987 and, since July 1, 1995, has 
served as vice president, operations.  Previously, from 1987 through June 
1995, Mr. Zinser held various management positions with the Company, 
including senior director, operations from July 1993 through June 1995.  Mr. 
Zinser received a M.B.A. from the University of California, Los Angeles. 
<PAGE>
     John N. Abelson, a founder of the Company, has served as a director 
since its inception.  Dr. Abelson, a molecular biologist, is a member 
of the National Academy of Sciences.  Since 1982, Dr. Abelson has been a 
member of the faculty of the Division of Biology at the California Institute 
of Technology where, from October 1989 until June 1995, he served as 
chairman.  Previously, Dr. Abelson was a member of the faculty in the 
Department of Chemistry at the University of California, San Diego.  Dr. 
Abelson received a Ph.D. in biophysics from The Johns Hopkins University and 
was a postdoctoral fellow at the Laboratory of Molecular Biology in 
Cambridge, England.  Dr. Abelson also serves as a director of The Agouron 
Institute. 

     Patricia M. Cloherty joined the Board in December 1988.  Since 1970, 
Ms. Cloherty has been associated with Patricof & Co. Ventures, Inc. 
(formerly Alan Patricof Associates, Inc.), a New York venture capital firm 
("Patricof"), and has been a general partner of its funds since 1973.  In 
1993, she was elected president of Patricof.  Ms. Cloherty also served as 
deputy administrator for the U.S. Small Business Administration in 1977 and 
1978.  Ms. Cloherty also serves on the board of directors of several private 
companies. 

     A.E. Cohen joined the Board in March 1992.  Mr. Cohen is an independent 
management consultant.  From 1957 until his retirement in January 1992, Mr. 
Cohen held various positions at Merck & Co., Inc., including senior vice 
president and president of the Merck Sharp & Dohme International Division. 
Currently, Mr. Cohen is the chairman of the board of Neurobiological 
Technologies, Inc. and is a member of the board of directors of Akzo N.V., 
Immunomedics, Inc., Teva Pharmaceutical Industries Ltd. and Vasomedical, 
Inc., all of which are public companies.  Mr. Cohen also serves on the board 
of directors of several private companies. 

     Michael E. Herman joined the Board in October 1992.  Mr. Herman is a 
private investor, as well as president and chief operating officer of the 
Kansas City Royals Baseball Team.  From October 1974 until his retirement in 
1990, Mr. Herman held various positions at Marion Laboratories, Inc. (now 
Hoechst Marion Roussel), including executive vice president and chief 
financial officer. Currently, Mr. Herman serves as chairman of the finance 
committee of the Ewing Marion Kauffman Foundation, a private foundation 
located in Kansas City, where from 1985 through 1990, he was the president 
and chief operating officer.  Mr. Herman is also a member of the board of 
directors of Cerner Corporation and Seafield Capital, both of which are 
public companies, and serves on the board of directors of several private 
companies. 

     Irving S. Johnson joined the Board in May 1989.  Dr. Johnson is an 
independent consultant in biomedical research working with numerous private 
companies.  From 1953 until his retirement in November 1988, Dr. Johnson 
held various positions at Eli Lilly and Company, including vice president of 
research from 1973 until 1988.  Dr. Johnson also served on several 
committees of the National Academy of Sciences, the Office of Technology 
Assessment and the National Institutes of Health.  Currently, he is a member 
of the board of directors of Allelix Biopharmaceuticals Inc. and Ligand 
Pharmaceuticals Incorporated, all of which are public companies.  Dr. 
Johnson received a Ph.D. in developmental biology from the University of 
Kansas. 

     Antonie T. Knoppers joined the Board in July 1991.  Dr. Knoppers is an 
independent management consultant.  From 1952 until his retirement in 1975, 
Dr. Knoppers held various positions at Merck & Co., Inc., including vice 
chairman of the board and president and chief operating officer.  Dr. 
Knoppers is a member of the board of directors of Centocor, Inc., a public 
biotechnology company.  In addition, he is a former chairman of the U.S. 
Council of the International Chamber of Commerce and a member of the 
advisory board of PaineWebber Development Corporation, an affiliate of 
PaineWebber Incorporated.  Dr. Knoppers received a M.D. from the University 
of Amsterdam and a Ph.D. from the University of Leiden, The Netherlands. 
<PAGE>
     Melvin I. Simon, a founder of the Company, has served as a director 
since its inception. Dr. Simon, a molecular geneticist, is a (member of the 
National Academy of Sciences.  Currently,  Dr. Simon is chairman of the 
Division of Biology at the California Institute of Technology where he has 
been a member of the faculty since 1982. Previously, Dr. Simon was a member 
of the faculty in the Department of Biology at the University of California, 
San Diego.  Dr. Simon received a Ph.D. in biochemistry from Brandeis 
University.  Dr. Simon also serves as a director of The Agouron Institute. 


Item 11.     EXECUTIVE COMPENSATION


Item 12.     SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT


Item 13.     CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS

     The information required under Part III, Items 10 (in part), 11, 12 and 
13 has been omitted from this report since the Company intends to file with 
the Securities and Exchange Commission, not later than 120 days after the 
close of its fiscal year, a definitive proxy statement prepared pursuant to 
Regulation 14A, which information is hereby incorporated by reference. 

<PAGE>
                                    PART IV


Item 14.     EXHIBITS, FINANCIAL STATEMENT SCHEDULES AND REPORTS ON FORM 8-K

(a)     List of documents filed as part of this report: 

        (1)     Financial Statements and Supplementary Data Reference is 
                made to the Index to Financial Statements and Schedules 
                under Item 8 in Part II hereof, where these documents are 
                listed. 
        (2)     Exhibits - see (c) below

(b)     Reports on Form 8-K

      A report on Form 8-K dated June 21, 1996 was filed during the fourth 
quarter of fiscal 1996.  Such report related to a binding letter of intent 
between the Company and Hoffmann-La Roche Inc. of Nutley, New Jersey and F. 
Hoffmann-La Roche Ltd. of Basel, Switzerland. 

(c)     Exhibits

     Exhibit
     Number                              Exhibit               
     -------      ----------------------------------------------------------

     3.1(b)       Articles of Incorporation (as Amended). 
     3.3(d)       Amended and Restated Bylaws (Restated June 17, 1991). 
     3.4(h)       Restated Articles of Incorporation (December 10, 1992). 
     4.1(h)       Restated Articles of Incorporation. 
     4.3(a)       Seaport Ventures, Inc. Warrant dated June 30, 1986. 
     10.33(n)     1990 Stock Option Plan (Restated November 2, 1995). 
     10.34(d)     Form of 1990 Incentive Stock Option Agreement. 
     10.35(d)     Form of 1990 Non-Statutory Stock Option Agreement--
                  Employee/Officer/ Director. 
     10.36(d)     Form of 1990 Non-Statutory Stock Option Agreement--
                  Consultant. 
     10.37(d)     1985 Stock Option Plan (Last Amended August 14, 1991). 
     10.38(d)     Form of 1985 Incentive Stock Option Agreement (Last 
                  Amended December 5, 1990). 
     10.39(d)     Form of 1985 Non-Statutory Stock Option Agreement--
                  Employee/Officer/ Director (Last Amended December 5, 
                  1990). 
     10.40(d)     Form of 1985 Stock Option Agreement--Consultant (Last 
                  Amended December 5, 1990). 
     10.41(e)     Business Loan Agreement and Promissory Note dated 
                  September 24, 1991 between the Company and First National 
                  Bank. 
     10.42(f)     Agouron Pharmaceuticals, Inc. 401(k) Plan (Amended August 
                  1992). 
     10.43(k)     Second Amendment and Restatement of Agreement One dated 
                  April 22, 1994 (effective December 18, 1992) between Japan 
                  Tobacco Inc. and the Company.  (Portions of the agreement 
                  receive confidential treatment pursuant to an application 
                  filed September 9, 1994; File No. 0-15609). 
     10.44(g)     Common Stock Purchase Agreement dated December 18, 1992 
                  between Japan Tobacco Inc. and the Company. 
     10.45(h)     Agouron Pharmaceuticals, Inc. Flexible Benefits Plan 
                  (December 10, 1992). 
     10.46(h)     Agouron Pharmaceuticals, Inc. Employee Stock Purchase Plan 
                  (October 15, 1992). 
<PAGE>
     Exhibit
     Number                              Exhibit               
     -------       ---------------------------------------------------------

     10.47(i)     Agreement dated June 8, 1993 between Syntex (U.S.A.) Inc. 
                  and the Company.  (Portions of the agreement receive 
                  confidential treatment pursuant to an application filed 
                  September 1, 1993; File No. 0-15609). 
     10.48(i)     Common Stock Purchase Agreement dated June 8, 1993 between 
                  Syntex Corporation and the Company. 
     10.49(c)     Office Lease dated March 16, 1990 between Nexus Science 
                  Centre--Torrey Pines Associates and the Company. 
     10.50(c)     First Amendment to Lease dated May 22, 1990 between Nexus 
                  Science Centre--Torrey Pines Associates and the Company. 
     10.51(d)     Second Amendment to Lease dated January, 1991 between 
                  Nexus Science Centre--Torrey Pines Associates and the 
                  Company. 
     10.52(j)     Agreement Two dated February 28, 1994 between Japan 
                  Tobacco Inc. and the Company.  (Portions of the agreement 
                  receive confidential treatment pursuant to an application 
                  filed April 25, 1994; File No. 0-15609). 
     10.53(j)     Agreement Three dated February 28, 1994 between Japan 
                  Tobacco Inc. and the Company.  (Portions of the agreement 
                  receive confidential treatment pursuant to an application 
                  filed April 25, 1994; File No. 0-15609). 
     10.54(l)     Development and License Agreement dated December 1, 1994 
                  between Japan Tobacco Inc. and the Company (Portions of 
                  the agreement receive confidential treatment pursuant to 
                  an application dated January 31, 1995). 
     10.55(l)     Third Amendment of Agreement One effective January 15, 
                  1995 between Japan Tobacco Inc. and the Company (Portions 
                  of the agreement receive confidential treatment pursuant 
                  to an application dated January 31, 1995). 
     10.56(m)     Amended and Restated Lease dated September 13, 1995 
                  between Health Science Properties, Inc. and the Company. 
     10.57(m)     Lease Amendment dated February 17, 1994 between Koll 
                  Hancock Torrey Pines and the Company. 
     10.58(n)     First Amendment to Development and License Agreement 
                  effective December 1, 1995 between Japan Tobacco Inc. and 
                  the Company.  (Confidential treatment has been requested 
                  for portionsof this agreement pursuant to an application 
                  dated January 31, 1996.  The underlying agreement was 
                  filed as Exhibit 10.54 on Form 10-Q for the period ended 
                  December 31, 1994, and portions thereof receive 
                  confidential treatment pursuant to an order of the 
                  Securities and Exchange Commission dated June 28, 1995.) 
     10.59(o)     First Amendment to Agreement Three effective February 29, 
                  1996 between Japan Tobacco, Inc. and the Company. 
     10.60(o)     Amendment effective January 1, 1996 to the Agouron 
                  Pharmaceuticals, Inc. 401(k) Plan. 
     10.61(p)     Binding Letter of Intent between Hoffmann-La Roche Inc. of 
                  Nutley, New Jersey, F. Hoffmann-La Roche Ltd. of Basel, 
                  Switzerland (Roche) and the registrant dated June 19, 
                  1996.  (Portions of the Letter of Intent receive 
                  confidential treatment pursuant to a request filed June 
                  21, 1996.) 
     10.62        Sub-sublease dated July 24, 1996, between ITT Residential 
                  Capital Serving Corporation and the Company. 
     23.1         Consent of Independent Accountants. 
     27           Financial Data Schedule.  (Exhibit 27 is submitted as an 
                  exhibit only in the electronic format of this Annual 
                  Report on Form 10-K submitted to the Securities and 
                  Exchange Commission.) 
<PAGE>
     Exhibit
     Number                              Exhibit               
     -------      ----------------------------------------------------------
     99           Important Factors Regarding Forward-Looking Statements. 

- ----------
     (a)     Incorporated by Reference to Form S-18 filed on March 20, 1987, 
             File No. 33-12110-LA. 
     (b)     Incorporated by Reference to Form 10-Q filed for the quarter 
             ended December 31, 1988. 
     (c)     Incorporated by Reference to Form 8-K filed on May 25, 1990 
             (Exhibits 10.49 and 10.50 originally filed as Exhibits 28.1 and
             28.2, respectively). 
     (d)     Incorporated by Reference to Form 10-K filed for the year 
             ended June 30, 1991 (Exhibit 10.51 originally filed as Exhibit 
             28.3). 
     (e)     Incorporated by Reference to Form S-1 filed on October 4, 1991, 
             File No. 33-43162. 
     (f)     Incorporated by Reference to Form 10-K filed for the year ended 
             June 30, 1992. 
     (g)     Incorporated by Reference to Form 8-K filed on December 30, 
             1992. 
     (h)     Incorporated by Reference to Form 10-Q filed for the quarter 
             ended December 31, 1992. 
     (i)     Incorporated by Reference to Form 10-K filed for the year ended 
             June 30, 1993. 
     (j)     Incorporated by Reference to Form 10-Q/A filed for the quarter 
             ended March 31, 1994. 
     (k)     Incorporated by Reference to Form 10-K filed for the year ended 
             June 30, 1994. 
     (l)     Incorporated by Reference to Form 10-Q filed for the quarter 
             ended December 31, 1994. 
     (m)     Incorporated by Reference to Form 10-K filed for the year ended 
             June 30, 1995. 
     (n)     Incorporated by Reference to Form 10-Q filed for the quarter 
             ended December 31, 1995. 
     (o)     Incorporated by Reference to Form 10-Q filed for the quarter 
             ended March 31, 1996. 
     (p)     Incorporated by Reference to Form 8-K filed on June 21, 1996. 


Note:     Certain previously filed exhibits are no longer being incorporated 
by reference (and therefore not numerically listed) as the underlying 
documents have either expired or are no longer material or relevant. 
<PAGE>
                                  Signatures

     Pursuant to the requirements of Section 13 or 15(d) of the Securities 
Exchange Act of 1934, the registrant has duly caused this report to be 
signed on its behalf by the undersigned, thereunto duly authorized. 


                                       AGOURON PHARMACEUTICALS, INC. 



September 16, 1996                     By:/s/ Peter Johnson
                                          Peter Johnson
                                          President, Chief Executive Officer
                                          and Director

     Pursuant to the requirements of the Securities Exchange Act of 1934, 
this report has been signed below by the following persons on behalf of the 
registrant and in the capacities and on the date indicated. 


Signature                            Title                       Date
- ---------                  --------------------------     ------------------
/s/ Peter Johnson          President, Chief Executive     September 16, 1996
                           Officer and Director

/s/ Steven S. Cowell       Vice President, Finance and    September 16, 1996
                           Chief Financial Officer

/s/ John N. Abelson        Director                       September 16, 1996

/s/ Patricia M. Cloherty   Director                       September 16, 1996

/s/ A. E. Cohen            Director                       September 16, 1996

/s/ Gary E. Friedman       Vice President, General        September 16, 1996
                           Counsel, Secretary and
                           Director

/s/ Michael E. Herman      Director                       September 16, 1996

/s/ Irving S. Johnson      Director                       September 16, 1996

/s/ Antonie T. Knoppers    Director                       September 16, 1996

/s/ Melvin I. Simon        Director                       September 16, 1996
<PAGE>

     Exhibit                                                       Page
     Number                    Exhibit                             Number
     -------      ----------------------------------------------   ------

     3.1(b)       Articles of Incorporation (as Amended). 
     3.3(d)       Amended and Restated Bylaws (Restated June 17, 
                  1991). 
     3.4(h)       Restated Articles of Incorporation (December
                  10, 1992). 
     4.1(h)       Restated Articles of Incorporation. 
     4.3(a)       Seaport Ventures, Inc. Warrant dated June 30, 
                  1986. 
     10.33(n)     1990 Stock Option Plan (Restated November 2, 
                  1995). 
     10.34(d)     Form of 1990 Incentive Stock Option Agreement. 
     10.35(d)     Form of 1990 Non-Statutory Stock Option 
                  Agreement--Employee/Officer/ Director. 
     10.36(d)     Form of 1990 Non-Statutory Stock Option 
                  Agreement--Consultant. 
     10.37(d)     1985 Stock Option Plan (Last Amended August 14, 
                  1991). 
     10.38(d)     Form of 1985 Incentive Stock Option Agreement
                  (Last Amended December 5, 1990). 
     10.39(d)     Form of 1985 Non-Statutory Stock Option 
                  Agreement--Employee/Officer/ Director (Last 
                  Amended December 5, 1990). 
     10.40(d)     Form of 1985 Stock Option Agreement--
                  Consultant (Last Amended December 5, 1990). 
     10.41(e)     Business Loan Agreement and Promissory Note 
                  dated September 24, 1991 between the Company 
                  and First National Bank. 
     10.42(f)     Agouron Pharmaceuticals, Inc. 401(k) Plan 
                  (Amended August 1992). 
     10.43(k)     Second Amendment and Restatement of Agreement 
                  One dated April 22, 1994 (effective December 18, 
                  1992) between Japan Tobacco Inc. and the Company. 
                  (Portions of the agreement receive confidential
                  treatment pursuant to an application filed 
                  September 9, 1994; File No. 0-15609). 
     10.44(g)     Common Stock Purchase Agreement dated December
                  18, 1992 between Japan Tobacco Inc. and the 
                  Company. 
     10.45(h)     Agouron Pharmaceuticals, Inc. Flexible Benefits
                  Plan (December 10, 1992). 
     10.46(h)     Agouron Pharmaceuticals, Inc. Employee Stock 
                  Purchase Plan (October 15, 1992). 
     10.47(i)     Agreement dated June 8, 1993 between Syntex 
                  (U.S.A.) Inc. and the Company.  (Portions of
                  the agreement receive confidential treatment 
                  pursuant to an application filed September 1, 
                  1993; File No. 0-15609). 
     10.48(i)     Common Stock Purchase Agreement dated June 8, 
                  1993 between Syntex Corporation and the Company. 
     10.49(c)     Office Lease dated March 16, 1990 between Nexus 
                  Science Centre--Torrey Pines Associates and the
                  Company. 
     10.50(c)     First Amendment to Lease dated May 22, 1990 
                  between Nexus Science Centre--Torrey Pines 
                  Associates and the Company. 
     10.51(d)     Second Amendment to Lease dated January, 1991
                  between Nexus Science Centre--Torrey Pines 
                  Associates and the Company. 
<PAGE>
     10.52(j)     Agreement Two dated February 28, 1994 between
                  Japan Tobacco Inc. and the Company.  (Portions 
                  of the agreement receive confidential treatment
                  pursuant to an application filed April 25, 1994; 
                  File No. 0-15609). 
     10.53(j)     Agreement Three dated February 28, 1994 between 
                  Japan Tobacco Inc. and the Company.  (Portions 
                  of the agreement receive confidential treatment
                  pursuant to an application filed April 25, 1994; 
                  File No. 0-15609). 
     10.54(l)     Development and License Agreement dated December
                  1, 1994 between Japan Tobacco Inc. and the Company
                  (Portions of the agreement receive confidential
                  treatment pursuant to an application dated 
                  January 31, 1995). 
     10.55(l)     Third Amendment of Agreement One effective January
                  15, 1995 between Japan Tobacco Inc. and the Company
                  (Portions of the agreement receive confidential 
                  treatment pursuant to an application dated January
                  31, 1995). 
     10.56(m)     Amended and Restated Lease dated September 13, 1995
                  between Health Science Properties, Inc. and the 
                  Company. 
     10.57(m)     Lease Amendment dated February 17, 1994 between
                  Koll Hancock Torrey Pines and the Company. 
     10.58(n)     First Amendment to Development and License 
                  Agreement effective December 1, 1995 between 
                  Japan Tobacco Inc. and the Company.  (Confidential
                  treatment has been requested for portionsof this 
                  agreement pursuant to an application dated January
                  31, 1996.  The underlying agreement was filed as 
                  Exhibit 10.54 on Form 10-Q for the period ended 
                  December 31, 1994, and portions thereof receive 
                  confidential treatment pursuant to an order of the 
                  Securities and Exchange Commission dated June 28, 
                  1995.) 
     10.59(o)     First Amendment to Agreement Three effective 
                  February 29, 1996 between Japan Tobacco, Inc. and
                  the Company. 
     10.60(o)     Amendment effective January 1, 1996 to the Agouron
                  Pharmaceuticals, Inc. 401(k) Plan. 
     10.61(p)     Binding Letter of Intent between Hoffmann-La 
                  Roche Inc. of Nutley, New Jersey, F. Hoffmann-La
                  Roche Ltd. of Basel, Switzerland (Roche) and the 
                  registrant dated June 19, 1996.  (Portions of the
                  Letter of Intent receive confidential treatment 
                  pursuant to a request filed June 21, 1996.) 
     10.62        Sub-sublease dated July 24, 1996, between ITT
                  Residential Capital Serving Corporation and 
                  the Company. 
     23.1         Consent of Independent Accountants. 
     27           Financial Data Schedule.  (Exhibit 27 is 
                  submitted as an exhibit only in the electronic 
                  format of this Annual Report on Form 10-K submitted 
                  to the Securities and Exchange Commission.) 
     99           Important Factors Regarding Forward-Looking 
                  Statements. 

- ----------
     (a)     Incorporated by Reference to Form S-18 filed on March 20, 1987, 
             File No. 33-12110-LA. 
     (b)     Incorporated by Reference to Form 10-Q filed for the quarter 
             ended December 31, 1988. 
     (c)     Incorporated by Reference to Form 8-K filed on May 25, 1990 
             (Exhibits 10.49 and 10.50 originally filed as Exhibits 28.1 and
             28.2, respectively). 
     (d)     Incorporated by Reference to Form 10-K filed for the year 
             ended June 30, 1991 (Exhibit 10.51 originally filed as Exhibit 
             28.3). 
     (e)     Incorporated by Reference to Form S-1 filed on October 4, 1991, 
             File No. 33-43162. 
     (f)     Incorporated by Reference to Form 10-K filed for the year ended 
             June 30, 1992. 
     (g)     Incorporated by Reference to Form 8-K filed on December 30, 
             1992. 
     (h)     Incorporated by Reference to Form 10-Q filed for the quarter 
             ended December 31, 1992. 
     (i)     Incorporated by Reference to Form 10-K filed for the year ended 
             June 30, 1993. 
     (j)     Incorporated by Reference to Form 10-Q/A filed for the quarter 
             ended March 31, 1994. 
     (k)     Incorporated by Reference to Form 10-K filed for the year ended 
             June 30, 1994. 
     (l)     Incorporated by Reference to Form 10-Q filed for the quarter 
             ended December 31, 1994. 
     (m)     Incorporated by Reference to Form 10-K filed for the year ended 
             June 30, 1995. 
     (n)     Incorporated by Reference to Form 10-Q filed for the quarter 
             ended December 31, 1995. 
     (o)     Incorporated by Reference to Form 10-Q filed for the quarter 
             ended March 31, 1996. 
     (p)     Incorporated by Reference to Form 8-K filed on June 21, 1996. 




<PAGE>
                                                                Exhibit 10.62
 .                            SUB-SUBLEASE      
     READ CAREFULLY, THIS AGREEMENT AFFECTS YOUR LEGAL RIGHTS
     
     1.     PARTIES
     
     This Sub-SubLease is entered into by and between ITT Residential Capital 
Serving Corporation, Sub-Sublandlord, and Agouron Pharmaceuticals, Sub-
Subtenant, as a Sub-Sublease under the Master Lease dated May 27, 1983, 
entered into by Torrey Executive Centre, Ltd. as Landlord and Bowest 
Corporation as Tenant and under the Sublease dated April 1, 1992 entered into 
by Bowest Corporation as Sublandlord and Sub-Sublandlord under this Sub-
Sublease as Subtenant; a copy of the Master Lease and Sublease are attached 
hereto as Exhibit A.  Sub-Sublandlord is the successor-in-interest to ITT 
Mortgage.
     
     2.     PROVISIONS CONSTITUTING SUB-SUBLEASE
     
          (a)     This Sub-Sublease is subject to all of the terms and 
conditions of the Master Lease and Sublease in Exhibit A and Sub-Subtenant 
shall assume and perform the obligations of Sub-Sublandlord and Subtenant in 
said Master Lease and Sublease, to the extent said terms and conditions are 
applicable to the Premises Sub-Subleased pursuant to this Sub-Sublease.  Sub-
Subtenant shall not commit or permit to be committed on the Premises any act 
or omission which shall violate any term or condition of the Master Lease or 
Sublease.
     
          (b)     All of the terms and conditions contained in the Exhibit A 
Master Lease and Sublease are incorporated herein, except for the terms and 
conditions as modified in paragraph 3 through 9 of this Sub-Sublease and the 
attached Addendum, as terms and conditions of this Sub-Sublease (with each 
reference therein to Landlord and Tenant and Sublandlord and Subtenant to be 
deemed to refer to Sub-Sublandlord and Sub-Subtenant) and, along with all of 
the following Sections set out in this Sub-Sublease, shall be the complete 
terms and conditions of this Sub-Sublease.
     
     3.     PREMISES
     
     Sub-Sublandlord leases to Sub-Subtenant and Sub-Subtenant hires from 
Sub-Sublandlord the following described Premises together with the 
appurtenances, situated in the City of La Jolla, County of San Diego, State 
of California, located at 3301 Torrey Pines Court, and further described as 
approximately 41,254 rentable square feet in a freestanding four story 
building.
     
     4.     RENTAL
     
     Sub-Subtenant shall pay to Sub-Sublandlord as rent for the Premises in 
advance on the first day of each calendar month of the term of this Sub-
Sublease without deduction, offset, prior notice or demand, in lawful money 
of the United States, the sum of Thirty Six Thousand Dollars and 00/100 
($36,000.00).  If the commencement date is not the first day of the month, or 
if the Sub-Sublessee termination date is not the last day of the month, a 
prorated monthly installment shall be paid at the then current rate for the 
fractional month during which the Sub-Sublease commences and/or terminates. 
See Addendum paragraph 1. 

     
     Receipt of $ Thirty Six Thousand Dollars and 00/100 is hereby 
acknowledged for rental for the seventh month, and the additional amount of $ 
Thirty Six Thousand Dollars and 00/100 as non-interest bearing security for 
performance under this Sub-Sublease.  In the event Sub-Subtenant has 
performed all of the terms and conditions of this Sub-Sublease throughout the 
term, upon Sub-Sublessee vacating the Premises, the amount paid as a security 
deposit shall be returned to Sub-Subtenant after first deducting any sums 
owing to Sub-Sublandlord.
<PAGE>
     5.     TERM
     
          (a)     The term of this Sub-Sublease shall be for a period of 37 
months commencing on August 1, 996, and ending on August 31, 1999.
     
          (b)     In the event Sub-Sublandlord is unable to deliver 
possession of the Premises at the commencement of the term, Sub-Sublandlord 
shall not be liable for any damage caused thereby, nor shall this Sub-
Sublease be void or avoidable but Sub-Subtenant shall not be liable for rent 
until such time as Sub-Sublandlord offers to deliver possession of the 
Premises to Sub-Subtenant, but the term thereof shall not be extended by such 
delay.  If Sub-Subtenant, with Sub-Sublandlord's consent, takes possession 
prior to the commencement of the term, Sub-Subtenant shall do so subject to 
all of the covenants and conditions hereof and shall pay rent for the period 
ending with the commencement of the term at the same rental as that 
prescribed for the first month of the term, prorated at the rate of 1/30th 
thereof per day. 
     
     6.     USE
     
     Subtenant shall use the Premises for general office use and for no other 
purpose without the prior written consent of Sub-Sublandlord and Landlord.
     
     Sub-Subtenant's business shall be established and conducted throughout 
the term hereof in a first class manner.  Sub-Subtenant shall not use the 
Premises for, or carry on, or permit to be carried on, any offensive, noisy 
or dangerous trade, business, manufacture or occupation nor permit any 
auction sale to be held or conducted on or about the Premises.  Sub-Subtenant 
shall not do or suffer anything to be done upon the Premises which will cause 
structural injury to the Premises or the building of which the Premises form 
a part.  The Premises shall not be overloaded and no machinery, apparatus or 
other appliance shall be used or operated in or upon the Premises which will 
in any manner injure, vibrate or shake the Premises or the building of which 
it is a part.  No use shall be made of the Premises which will in any way 
impair the efficient operation of the sprinkler system within the building 
containing the Premises.  No musical instrument of any sort, or any noise 
making device will be operated or allowed upon the Premises for the purpose 
of attracting trade or otherwise.  Sub-Subtenant shall not use or permit the 
use of the Premises or any part thereof for any purpose which will increase 
the existing rate of insurance upon the building in which the Premises are 
located, or cause a cancellation of any insurance policy covering the 
building or any part thereof.  If any act on the part of Sub-Subtenant or use 
of the Premises by Sub-Subtenant shall cause, directly or indirectly, any 
increase of Sub-Sublandlord's insurance expense, said additional expense 
shall be paid by Sub-Subtenant to Sub-Sublandlord upon demand.  No such 
payment by Sub-Subtenant shall limit Sub-Sublandlord in the exercise of any 
other rights or remedies, or constitute a waiver of Sub-Sublandlord's right 
to require Sub-Subtenant to discontinue such act or use.
     
     7.     NOTICES
     
     All notices or demands of any kind required or desired to be given by 
Sub-Sublandlord or Sub-Subtenant thereunder shall be in writing and shall be 
deemed delivered forty-eight (48) hours after depositing the notice or demand 
in the United States mail, certified or registered, postage prepaid, at the 
addresses set forth after the signatures at the end of this Sub-Sublease. 
All rent and other payments due under the Sub-Sublease shall be made by Sub-
Subtenant to Sub-Sublandlord at the appropriate address.
<PAGE>     
     8.     SEE ADDENDUM     
     
     9.     Nothing contained in this Sub-Sublease shall be construed to 
release Tenant or Subtenant from any obligations to perform the terms, 
conditions and covenants of the Sublease or Master Lease. 

     
     Dated:  July 24, 1996
     
     Sub-Sublandlord:  ITT CELCO       Sub-Subtenant: Agouron 
                                       Pharmaceuticals, Inc.
     
     By: /s/ ITT CELCO                 By: /s/ Glenn Zinser
                                           Vice President
     
                                       By: /s/ Gary Friedman
                                           Vice President
     
     Address: 645 Mayville Center      Address: 10350 N. Torrey Pines Rd.,
     St. Louis, MO 63144               La Jolla, CA 92037
     
     
     The undersigned, Landlord under the Master Lease, attached as Exhibit A 
and Sublandlord under the Sublease attached as Exhibit A, hereby consent to 
the sub-subletting of the Premises described herein on the terms and 
conditions contained in this Sub-Sublease.  This consent shall apply only to 
this Sub-Sublease and shall not be deemed to be a consent to any other Sub-
Sublease.
     
                                      Successor in Interest to ITT Mortgage - 
                                        Bowest
     Dated: July 24, 1996             Sublandlord:  ITT CELCO
                                        
     
                                      By: /s/ Thomas Stiffler
     
                                      Landlord:  Torrey Pines Centre, Ltd.
     
                                      By: /s/ Torrey Pines Centre, Ltd.
     
                                      By: /s/
     
     (If Sub-Sublandlord or Sub-Subtenant is a corporation, the corporate 
seal must be affixed and the authorized officers must sign on behalf of the 
corporation.  The Sub-Sublease must be executed by the President or a Vice 
President and the Secretary or Assistant Secretary unless the Bylaws or a 
Resolution of the Board of Directors shall otherwise provide, in which event 
the Bylaws or a certified copy of the Resolution, as the case may be must be 
furnished.)
     
     This Sub-Sublease has been prepared for submission to your attorney who 
will review the document and assist you to determine whether your legal 
rights are adequately protected.  Colliers Iliff Thorn is not authorized to 
give legal or tax advice; no representation or recommendation is made by 
Colliers Iliff Thorn or its agents or employees as to the legal sufficiency, 
legal effect or tax consequences of this document or any transaction relating 
thereto.  These are questions for your attorney, with whom you should consult 
before signing this document.
     
<PAGE>
                         ADDENDUM TO SUB-SUBLEASE
     
     Addendum to the Sub-Sublease by and between ITT Residential Capital 
Servicing Corporation ("Sub-Sublandlord") and Agouron Pharmaceuticals ("Sub-
Subtenant"), commencing August 1, 1996 and terminating August 31, 1999.
     
     1.     RENT DUE:
     
            Months               Total Monthly Rent Due
            ------               ----------------------
            1-6                  $     0.00
            7-32                 $36,000.00
            33-37                $30,000.00
     
          During months one (1) through six (6), Sub-Subtenant will only be 
responsible for paying utility and janitorial expenses for the Premises.
     
     2.     TENANT IMPROVEMENTS:
     
          Sub-Sublandlord shall cause the Premises to be in clean and swept 
condition.  Additionally, HVAC, elevator and other building systems will be 
in good working order and adequate for normal office use upon commencement of 
the Sub-Sublease.  Sub-Subtenant shall be responsible for all governmental 
permits necessary to operate within the Premises.
     
          Sub-Sublandlord shall not be responsible for the costs of any 
tenant improvements constructed by Sub-Subtenant's.  Sub-Sublandlord shall 
have the right to approve the tenant improvements to be made by Sub-
Subtenant.
     
     3.     OPERATING EXPENSES:
     
          Sub-Subtenant shall only be responsible for utility and janitorial 
expenses for the Premises.  Sub-Sublandlord will be responsible for all other 
building and project operating expenses during the term of the Sub-Sublease.
     
     4.     PARKING:
     
          Sub-Sublandlord will provide Sub-Subtenant with the exclusive use 
of 104 parking spaces in the subterranean parking garage at no cost during 
the Sub-Sublease term.
     
     5.     SUBLANDLORD AND SUB-SUBLANDLORD TO PAY RENT:
     
          The parties to this Sub-Sublease acknowledge that in order to 
protect this Sub-Sublease, Sub-Sublandlord and Sublandlord must pay the rent 
due and owing under the Sublease and Master Lease.  Sub-Sublandlord and 
Sublandlord hereby covenant that they shall pay the rent under the Sublease 
and Master Lease for the term of the Sublease and Master Lease respectively, 
and satisfy and perform all other obligations thereunder.  Sub-Subtenant 
agrees that upon notice from Sublandlord or Landlord, that Sub-Sublandlord is 
in default under the Sublease or that Tenant is in default under the Master 
Lease, Sub-Subtenant shall pay the rent due under this Sub-Sublease directly 
to the Landlord.
<PAGE>
     6.     SIGNAGE:
     
          Any signage required by Sub-Subtenant will be subject to Landlord's 
approval, which shall not be unreasonably withheld and subject to Sub-
Subtenant's receipt of all necessary approvals for such signage.  Sub-
Subtenant shall be responsible for all costs associated with said signage, 
including fabrication, installation, maintenance and removal.
     
     7.     MASTER LEASE PROVISIONS:
     
          Sub-Subtenant will have the right to exercise the option to extend 
and any expansion rights contained in the Master Lease, dated May 27, 1983. 
Additionally, to the extend provided in the Master Lease, or Sublease, Sub-
Subtenant's employees will have the use of the amenities associated with the 
Premises (i.e., pool, workout room, racquetball courts, etc.).



<PAGE>
                                                                Exhibit 23.1



                  CONSENT OF INDEPENDENT ACCOUNTANTS



We hereby consent to the incorporation by reference in the Registration 
Statement on Form S-8 (No. 33-64415) of Agouron Pharmaceuticals, Inc. of 
our report dated August 7, 1996 appearing on page F-1 of this Annual Report 
on Form 10-K. 






/s/ PRICE WATERHOUSE LLP

San Diego, California
September 16, 1996



<TABLE> <S> <C>


<PAGE>
<ARTICLE> 5
<LEGEND>
THIS SCHEDULE CONTAINS SUMMAY FINANCIAL INFORMATION EXTRACTED FROM THE 
BALANCE SHEET AND THE STATEMENT OF OPERATIONS AND IS QUALIFIED IN ITS 
ENTIRETY BY REFERENCE TO SUCH FINANCIAL STATEMENTS.
</LEGEND>
<MULTIPLIER> 1,000
            
<S>                                  <C>
<PERIOD-TYPE>                         12-MOS
<FISCAL-YEAR-END>                            JUN-30-1996
<PERIOD-END>                                 JUN-30-1996
<CASH>                                            16,451
<SECURITIES>                                      74,424
<RECEIVABLES>                                        613
<ALLOWANCES>                                           0
<INVENTORY>                                            0
<CURRENT-ASSETS>                                  93,288
<PP&E>                                            20,646
<DEPRECIATION>                                    13,710
<TOTAL-ASSETS>                                   100,224
<CURRENT-LIABILITIES>                             22,907
<BONDS>                                                0
<COMMON>                                         158,628
                                  0
                                            0
<OTHER-SE>                                       (83,045)
<TOTAL-LIABILITY-AND-EQUITY>                     100,224
<SALES>                                                0
<TOTAL-REVENUES>                                  55,955
<CGS>                                                  0
<TOTAL-COSTS>                                     51,099
<OTHER-EXPENSES>                                  28,927
<LOSS-PROVISION>                                       0
<INTEREST-EXPENSE>                                   228
<INCOME-PRETAX>                                  (19,523)
<INCOME-TAX>                                           0
<INCOME-CONTINUING>                              (19,523)
<DISCONTINUED>                                         0
<EXTRAORDINARY>                                        0
<CHANGES>                                              0
<NET-INCOME>                                     (19,523)
<EPS-PRIMARY>                                      (1.98)
<EPS-DILUTED>                                      (1.98)
        



</TABLE>


<PAGE>
                                                                 Exhibit 99

                          Agouron Pharmaceuticals, Inc.
                          Important Factors Regarding
                          Forward-Looking Statements


The following factors, among others, could cause actual results to differ 
materially from those contained in forward-looking statements made in this 
report and presented elsewhere by management from time to time.  Reference is
also made to the "Risk Factors" described in the Company's Prospectus dated 
July 26, 1996.

Uncertainty of Product Development:  The Company has not yet completed the 
development of any products and does not expect to have any products 
commercially available until calendar 1997, if at all.  There can be no 
assurance that further research and development will be successful or will 
result in drugs that will qualify for approval by regulatory authorities for 
commercial sale.

Uncertainty Associated with Clinical Testing:  Historical results of clinical 
testing of VIRACEPT (TM) and THYMITAQ (TM) are not necessarily predictive of 
future results. There can be no assurance that clinical studies of products 
under development will demonstrate the safety and efficacy of such products. 
The failure to adequately demonstrate the safety and efficacy of a 
therapeutic product could delay or prevent regulatory approval of the 
product.  There can be no assurance that unacceptable toxicities or side 
effects will not occur at any time in the course of human clinical trials or 
commercial use of the Company's drugs.  The appearance of any such 
unacceptable toxicities or side effects could interrupt, limit, delay or 
abort the development of any of the Company's drugs or, if previously 
approved, necessitate their withdrawal from the market.  Futhermore, there 
can be no assurance that disease resistance will not limit the efficacy of 
VIRACEPT or other of the Company's drugs, if any.  Delays in planned patient 
enrollment in the Company's current clinical trials or future clinical trials 
may result in increased costs, program delays 
or both.

History of Operating Losses:  The Company has not generated revenues from the 
commercialization of any products and expects to incur substantial net 
operating losses during the next few years.  There can be no assurance that 
the Company will ever achieve product revenues or profitable operations. 

Additional Financing Requirements and Access to Capital:  Additional funding 
may be required for future working capital and other general corporate needs. 
No assurance can be given that additional financing will be available when 
needed or on terms acceptable to the Company.  If adequate funds are not 
available, the Company may be required to delay or eliminate expenditures for 
certain of its programs or to license third parties to commercialize products 
or technologies that the Company would otherwise seek to develop and 
commercialize itself.

Dependence on Others:  The Company's strategy for development and 
commercialization of certain of its products entails entering into various 
arrangements with corporate partners, licensees and others.  There can be no 
assurance that any revenues or profits will be derived from such 
arrangements, that any of the Company's current strategic arrangements will 
be continued, or that the Company will be able to enter into future 
collaborations.

Lack of Manufacturing Capabilities:  The Company has not yet manufactured its 
product candidates in commercial quantities under current Good Manufacturing 
Practices.  No assurance can be given that the Company, on a timely basis, 
will be able to make the  transition to commercial production successfully or 
be able to arrange for contract manufacturing.

<PAGE>
Lack of Sales and Marketing Capabilities:  The Company has no experience in 
the sales, marketing and distribution of pharmaceutical products.  There can 
be no assurance that the Company will be able to establish sales, marketing 
and distribution capabilities or make arrangements with its collaborators, 
licensees or others to perform such activities or that such efforts will be 
successful.

Patents and Proprietary Technology:  No assurance can be given that the 
Company's patent applications will issue as patents or that any patents that 
may be issued will provide the Company with adequate protection for the 
covered products or technology.  Additionally, there can be no assurance that 
the Company's confidentiality agreements will adequately protect its trade 
secrets, know-how or other proprietary information.  Further, there can be no 
assurance that the Company's activities will not infringe on the patents or 
proprietary rights of others or that the Company will be able to obtain 
licenses to any technology that it may require to conduct its business or 
that, if obtainable, such technology can be licensed at a reasonable cost.

Technological Change and Competition:  There can be no assurance that 
competitors will not succeed in developing technologies and products that are 
more effective than any which have been or are being developed by the Company 
or which would render the Company's technology and products obsolete and 
noncompetitive.  Many of the Company's competitors have substantially greater 
financial and technical resources and production, marketing and development 
capabilities and experience than the Company.  Accordingly, certain of the 
Company's competitors may succeed in obtaining regulatory approval for 
products more rapidly or effectively than the Company.  If the Company 
commences commercial sales of its products, it will also be competing with 
respect to manufacturing efficiency and sales and marketing capabilities, 
areas in which it currently has no experience.

Volatility of Stock Price:  The market price of the Common Stock has in 
recent years fluctuated significantly, and it is likely that the price of 
Common Stock will fluctuate in the future.  Announcements by the Company or 
others regarding its existing and future collaborations, results of clinical 
trails, scientific discoveries, technological innovations, commercial 
products, patents or proprietary rights or regulatory actions may have a 
significant adverse effect on the market price of the Common Stock. 
Fluctuations in financial performance from period to period also may have a 
significant impact on the market price of the Common Stock.

Government Regulation:  Preclinical studies, clinical trials and the 
production and marketing of the Company's products and its ongoing research 
and development activities are subject to regulation by numerous governmental 
authorities in the United States and other countries.  If regulatory approval 
of a drug is obtained, such approval may involve limitations and restrictions 
on the drug's use.  Failure of the Company to comply with applicable 
regulatory requirements can, among other things, result in fines, suspension 
of regulatory approvals or product recalls.  Additionally, the Company is or 
may become subject to various federal, state and local laws, regulations and 
recommendations relating to safe working conditionsand the use and disposal 
of hazardous or potentially hazardous substances.  The Company is unable to 
predict the extent of restrictions that might arise from any governmental or 
administrative action. 

Uncertainty of Third-Party Reimbursement and Product Pricing:  The Company's 
ability to commercialize products successfully will depend in part on the 
availability of reimbursement of the costs of such products and related 
treatments at acceptable levels from government authorities, private health 
insurers and other organizations, such as health maintenance organizations 
("HMOs"). There can be no assurance that reimbursement in the United States 
or foreign countries will be available for any products the Company may 
develop or, if available, will not be decreased in the future, or that 
reimbursement amounts will not reduce the demand for, or the price of, the 
Company's products, thereby adversely affecting the Company's business. 
<PAGE>
Product Liability; Limited Insurance Coverage: The testing, marketing and 
sale of human health care products entail an inherent risk of allegations of 
product liability and there can be no assurance that product liability claims 
will not be asserted against the Company. There can be no assurance that the 
Company will be able to obtain or maintain product liability insurance on 
acceptable terms or that such insurance will provide adequate coverage 
against any potential claims.

Use of Hazardous Materials:  The Company's research and development 
activities involve the controlled use of hazardous materials, chemicals, 
viruses and various radioactive compounds. Although the Company believes that 
its safety procedures for handling and disposing of such materials comply 
with the standards prescribed by state and federal regulations, the risk of 
accidental contamination or injury from these materials cannot be completely 
eliminated. In the event of such an accident, the Company could be held 
liable for any damages that result and any liability could have a material 
adverse effect on the Company. 

Attraction and Retention of Personnel:  The future success of the Company 
will depend in large part on its ability to continue to attract and retain 
highly qualified scientific, technical and managerial personnel. Competition 
for such personnel is intense and there can be no assurance that Agouron will 
be able to attract and retain the personnel necessary for the development of 
its business.  The loss of or failure to recruit scientific, technical and 
managerial personnel could have a material adverse effect on the Company. 
<PAGE>


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