AMYLIN PHARMACEUTICALS INC
S-3/A, 1999-11-23
PHARMACEUTICAL PREPARATIONS
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   AS FILED WITH THE SECURITIES AND EXCHANGE COMMISSION ON NOVEMBER 23, 1999



                                                      REGISTRATION NO. 333-87033

- --------------------------------------------------------------------------------
- --------------------------------------------------------------------------------

                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549
                            ------------------------


                                AMENDMENT NO. 1


                                       TO


                                    FORM S-3
                             REGISTRATION STATEMENT
                                     UNDER
                           THE SECURITIES ACT OF 1933
                            ------------------------

                          AMYLIN PHARMACEUTICALS, INC.
             (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)

<TABLE>
<S>                                                 <C>
                     DELAWARE                                           33-0266089
           (STATE OR OTHER JURISDICTION                              (I.R.S. EMPLOYER
         OF INCORPORATION OR ORGANIZATION)                        IDENTIFICATION NUMBER)
</TABLE>

                            9373 TOWNE CENTRE DRIVE
                          SAN DIEGO, CALIFORNIA 92121
                                 (858) 552-2200
  (ADDRESS, INCLUDING ZIP CODE, AND TELEPHONE NUMBER, INCLUDING AREA CODE, OF
                   REGISTRANT'S PRINCIPAL EXECUTIVE OFFICES)

                              JOSEPH C. COOK, JR.
               CHAIRMAN OF THE BOARD AND CHIEF EXECUTIVE OFFICER
                          AMYLIN PHARMACEUTICALS, INC.
                            9373 TOWNE CENTRE DRIVE
                          SAN DIEGO, CALIFORNIA 92121
                                 (858) 552-2200
 (NAME, ADDRESS, INCLUDING ZIP CODE, AND TELEPHONE NUMBER, INCLUDING AREA CODE,
                             OF AGENT FOR SERVICE)

                                   COPIES TO:

                              THOMAS A. COLL, ESQ.
                               COOLEY GODWARD LLP
                        4365 EXECUTIVE DRIVE, SUITE 1100
                              SAN DIEGO, CA 92121
                                 (858) 550-6000

        APPROXIMATE DATE OF COMMENCEMENT OF PROPOSED SALE TO THE PUBLIC:
   From time to time after the effective date of this Registration Statement.

    If the only securities being registered on this Form are being offered
pursuant to dividend or interest reinvestment plans, please check the following
box. [ ]

    If any of the securities being registered on this Form are to be offered on
a delayed or continuous basis pursuant to Rule 415 under the Securities Act of
1933, other than securities offered only in connection with dividend or interest
reinvestment plans, check the following box. [X]

    If this Form is filed to register additional securities for an offering
pursuant to Rule 462(b) under the Securities Act, please check the following box
and list the Securities Act registration statement number of the earlier
effective registration statement for the same offering. [ ]

    If this Form is a post-effective amendment filed pursuant to Rule 462(c)
under the Securities Act, check the following box and list the Securities Act
registration statement number of the earlier effective registration statement
for the same offering. [ ]

    If delivery of the prospectus is expected to be made pursuant to Rule 434,
please check the following box. [ ]

                        CALCULATION OF REGISTRATION FEE


<TABLE>
<S>                                       <C>                  <C>                   <C>                   <C>
- ------------------------------------------------------------------------------------------------------------------------------
- ------------------------------------------------------------------------------------------------------------------------------
                                                                 PROPOSED MAXIMUM      PROPOSED MAXIMUM
         TITLE OF EACH CLASS OF                AMOUNT TO          OFFERING PRICE      AGGREGATE OFFERING        AMOUNT OF
      SECURITIES TO BE REGISTERED            BE REGISTERED         PER SHARE(1)            PRICE(1)        REGISTRATION FEE(2)
- ------------------------------------------------------------------------------------------------------------------------------
Common Stock, $.001 par value...........      12,594,009             $3.59375           $45,259,719.85         $12,582.21
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- ------------------------------------------------------------------------------------------------------------------------------
</TABLE>


(1) Estimated in accordance with Rule 457(c) of the Securities Act of 1933
    solely for the purpose of computing the amount of the registration fee based
    on the average of the high and low prices of the Registrant's Common Stock
    as reported on the Nasdaq SmallCap Market on September 7, 1999.


(2) Previously paid.


    THE REGISTRANT HEREBY AMENDS THIS REGISTRATION STATEMENT ON SUCH DATE OR
DATES AS MAY BE NECESSARY TO DELAY ITS EFFECTIVE DATE UNTIL THE REGISTRANT SHALL
FILE A FURTHER AMENDMENT THAT SPECIFICALLY STATES THAT THIS REGISTRATION
STATEMENT SHALL THEREAFTER BECOME EFFECTIVE IN ACCORDANCE WITH SECTION 8(a) OF
THE SECURITIES ACT OR UNTIL THE REGISTRATION STATEMENT SHALL BECOME EFFECTIVE ON
SUCH DATE AS THE COMMISSION, ACTING PURSUANT TO SAID SECTION 8(a), MAY
DETERMINE.
- --------------------------------------------------------------------------------
- --------------------------------------------------------------------------------
<PAGE>   2

         THE INFORMATION IN THIS PROSPECTUS IS NOT COMPLETE AND MAY BE CHANGED.
         WE MAY NOT SELL THESE SECURITIES UNTIL THE REGISTRATION STATEMENT FILED
         WITH THE SECURITIES AND EXCHANGE COMMISSION IS EFFECTIVE. THIS
         PROSPECTUS IS NOT AN OFFER TO SELL THESE SECURITIES AND IT IS NOT
         SOLICITING AN OFFER TO BUY THESE SECURITIES IN ANY STATE WHERE THE
         OFFER OR SALE IS NOT PERMITTED.


                 SUBJECT TO COMPLETION, DATED NOVEMBER 23, 1999


PROSPECTUS

                               12,594,009 SHARES

                          AMYLIN PHARMACEUTICALS, INC.

                                  COMMON STOCK

                           -------------------------


     We are registering for resale 12,594,009 shares of our common stock. The
security holders identified in this prospectus may offer the shares registered
for resale from time to time. We will not receive any proceeds from the security
holders' sale of their shares of our common stock.



     For a summary of the method of distribution of the resale shares, see page
19 of this prospectus.



     Our common stock is currently traded on the Nasdaq SmallCap Market under
the symbol "AMLN." On November 22, 1999, the last reported sales price of a
share of Amylin Pharmaceuticals, Inc. common stock on the Nasdaq SmallCap Market
was $7.938 per share.


                           -------------------------


         INVESTMENT IN OUR COMMON STOCK INVOLVES A HIGH DEGREE OF RISK.


           SEE "RISK FACTORS" BEGINNING ON PAGE 6 OF THIS PROSPECTUS.


                           -------------------------

NEITHER THE SECURITIES AND EXCHANGE COMMISSION NOR ANY STATE SECURITIES
COMMISSION HAS APPROVED OR DISAPPROVED OF THESE SECURITIES OR PASSED UPON THE
ADEQUACY OR ACCURACY OF THIS PROSPECTUS. ANY REPRESENTATION TO THE CONTRARY IS A
CRIMINAL OFFENSE.


               The date of this Prospectus is November   , 1999.

<PAGE>   3


     THIS PROSPECTUS IS PART OF A REGISTRATION STATEMENT WE FILED WITH THE
SECURITIES AND EXCHANGE COMMISSION. YOU SHOULD RELY ONLY ON THE INFORMATION
CONTAINED IN OR INCORPORATED BY REFERENCE IN THIS PROSPECTUS. THE SEC ALLOWS US
TO "INCORPORATE BY REFERENCE" INFORMATION THAT WE FILE WITH THEM, WHICH MEANS
THAT WE CAN DISCLOSE IMPORTANT INFORMATION TO YOU BY REFERRING YOU TO THOSE
DOCUMENTS. THE INFORMATION INCORPORATED BY REFERENCE IS CONSIDERED TO BE PART OF
THIS PROSPECTUS, AND INFORMATION THAT WE FILE LATER WITH THE SEC WILL
AUTOMATICALLY UPDATE AND SUPERSEDE THIS INFORMATION. WE HAVE NOT AUTHORIZED
ANYONE ELSE TO PROVIDE YOU WITH DIFFERENT INFORMATION. WE ARE NOT MAKING AN
OFFER OF THESE SECURITIES IN ANY STATE WHERE THE OFFER IS NOT PERMITTED. YOU
SHOULD NOT ASSUME THAT THE INFORMATION IN THIS PROSPECTUS IS ACCURATE AS OF ANY
DATE OTHER THAN THE DATE PROVIDED ON THE FRONT PAGE OF THIS PROSPECTUS,
REGARDLESS OF THE TIME OF DELIVERY OF THIS PROSPECTUS OR ANY SALE OF COMMON
STOCK.




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                                  OUR BUSINESS


     You should read the following summary together with the more detailed
information regarding our company, our common stock and our financial statements
and notes to those statements appearing elsewhere in this prospectus or
incorporated here by reference. References in this prospectus to "Amylin,"
"Amylin Pharmaceuticals," "our company," "we," "our," and "us" refer to Amylin
Pharmaceuticals, Inc.



     We are a development pharmaceutical company focused on metabolic disorders
and specializing in preclinical characterization of lead molecules and
demonstration of proof of principle in humans. We have pioneered research of the
hormone amylin and we are developing SYMLIN(TM) (pramlintide acetate), our
patented synthetic analog of human amylin, for the treatment of type 1 diabetes
and insulin-using type 2 diabetes. We are also evaluating AC2993 (synthetic
exendin-4), our second diabetes drug candidate, as a potential treatment for
type 2 diabetes and related metabolic disorders. Amylin is currently engaged in
partnership discussions for SYMLIN and AC2993.



SYMLIN CLINICAL TRIAL PROGRAM



     We designed the SYMLIN Phase 3 program to evaluate the safety and efficacy
of administration of SYMLIN for 6 months, 1 year, or longer. This program
comprises six double-blind, placebo-controlled studies (two in type 1 diabetes
in the US, two in type 2 diabetes in the US, and one each in type 1 and type 2
diabetes in Europe/Canada), and two longer term open-label, safety studies. We
conducted each of the double-blind studies to explore the effects of SYMLIN
administration (in addition to insulin) on metabolic control in people with
diabetes. We have reported results from all six double-blind Phase 3 studies. To
date, over 3,500 people have received SYMLIN in our clinical trials.



     Type 1, or juvenile onset, diabetes typically involves rapid deterioration
of pancreatic beta cell function resulting from autoimmune destruction of beta
cells. Approximately 2 million people in North America and Western Europe have
type 1 diabetes. These people have limited treatment options and require daily
insulin injections and careful attention to diet and exercise. Type 1 diabetes
is not usually helped by oral medications.



     Type 2, or adult onset, diabetes is a progressive disorder. Approximately
19 million people in North America and Western Europe have been diagnosed with
type 2 diabetes. People with type 2 diabetes initially are able to manage their
diabetes with diet, exercise, and/or oral diabetes medications. Over time many
people need injections of insulin each day to enable their bodies to metabolize
and store food. Amylin estimates that approximately 3.3 million people with type
2 diabetes in North America and Western Europe have progressed to a stage of
this disease that requires them to use multiple insulin injections each day.



Initial US Phase 3 results



     In August 1997, we reported the results of a one-year Phase 3 clinical
study in people with type 1 diabetes conducted in the US. SYMLIN recipients in
this study achieved a statistically significant decrease in the primary glucose
control endpoint compared with those study participants who received insulin
alone. These results were achieved without an increase in the frequency of
patient-reported severe hypoglycemic events. In addition, patients receiving
SYMLIN achieved significant weight loss.



     In August 1997, we also reported the results of a one-year Phase 3 study in
insulin-using type 2 patients. The mean average reduction of the primary glucose
control endpoint for patients receiving SYMLIN was significantly reduced at 13
and 26 weeks, but did not achieve statistical significance compared with study
participants who received insulin alone at one year. SYMLIN


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administration resulted in statistically significant weight loss compared with
those receiving insulin plus placebo.



European/Canadian Phase 3 results



     In October 1998, we announced results from two six-month Phase 3 European/
Canadian studies of SYMLIN, one in type 1 diabetes and one in insulin-using type
2 diabetes. In the study involving people with type 1 diabetes, two of the three
dosages studied achieved statistical significance, but neither of these dosages
had been selected as the primary arm for statistical analysis for regulatory
purposes. Unexpectedly, the effect on the primary glucose control endpoint
observed in the group who received the highest SYMLIN dosage did not reach
statistical significance. As a consequence, under the procedure specified in the
statistical analysis plan, the results from this study did not meet the
regulatory requirements to support a new drug application (NDA).



     In the European/Canadian study involving people with type 2 diabetes, the
results for two of the three dosage groups, including the highest dosage, were
not statistically different from the insulin only group. The results for a third
dosage group that received SYMLIN were significantly different from placebo. As
with the European/Canadian type 1 study, the highest total daily dosage group
had been designated in advance as the primary arm and did not achieve
statistical significance. Thus, the regulatory requirements for an NDA filing
were not met.



Additional analyses of first four Phase 3 studies



     Additional analyses of the data from Amylin's first four SYMLIN Phase 3
studies led to the observation that patients that administered SYMLIN together
with insulin and who achieved a reduction of hemoglobin A1c (HbA1c), the primary
glucose control endpoint, of at least 0.5% after four weeks of therapy had lower
HbA1c concentrations on average than the population of study participants as a
whole at the end of the study. These participants, designated by Amylin as
glycemic "responders", achieved average reductions in HbA1c concentrations that
were significantly higher than those participants that were not responders.


August 1999 Phase 3 results


     In August 1999, the Company announced that SYMLIN produced a statistically
significant lowering of the primary glucose control endpoint in a one-year study
in people with type 2 diabetes who use insulin. Additionally, study participants
who received SYMLIN experienced a statistically significant reduction in body
weight. As observed in previous studies of SYMLIN, the glycemic "responder"
rate, which was predefined in this study, in the SYMLIN group was approximately
twice that of the control group.



November 1999 Phase 3 results



     In November 1999, we announced that SYMLIN produced a statistically
significant lowering of the primary glucose control endpoint in a one-year,
pivotal Phase 3 clinical study in type 1 diabetes. For participants who had
SYMLIN added to their insulin regimens, the primary glucose control endpoint was
significantly improved at 6 months, compared to those who received insulin
alone. Additionally, to better understand the effects of SYMLIN independent of
the effects of insulin, a "stable insulin" group was predefined as those
participants who did not vary their insulin usage by more than 10% from
baseline. SYMLIN recipients in the "stable insulin" group achieved a reduction
in HbA1c of 0.7% at one year. As observed in previous studies of SYMLIN, the
glycemic "responder" rate, which was predefined in this study, in the SYMLIN
group was approximately twice that of the insulin alone group. In addition,
SYMLIN responders lost weight compared to the insulin alone group, who gained
weight.


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AC2993 CLINICAL TRIAL PROGRAM


     Our second drug product candidate, AC2993 (synthetic exendin-4), is in
Phase 2 evaluation for the treatment of people with type 2 diabetes. We have
demonstrated that AC2993 is biologically active in animal models when
administered via noninjectable routes.



RECENT APPOINTMENTS TO OUR BOARD OF DIRECTORS



     In July, August and September 1999, we elected Vaughn D. Bryson, Jay S.
Skyler, M.D. and Donald H. Rumsfeld, respectively, to our Board of Directors.
Mr. Bryson was a thirty-two year employee of Eli Lilly and Company and served as
its President and Chief Executive Officer from 1991 to 1993. He also served as
Eli Lilly's Executive Vice President from 1986 until 1991, and served as a
member of Lilly's Board of Directors from 1984 until his retirement in 1993.


     Dr. Skyler is a Professor of Medicine, Pediatrics, and Psychology and
Co-Director of the Behavioral Medicine Research Center at the University of
Miami in Florida. He is also Director of the Operations Coordinating Center for
the National Institute of Diabetes & Digestive & Kidney Diseases Diabetes
Prevention Trial in Type 1 Diabetes. Dr. Skyler has also served as President of
the American Diabetes Association, and is current Vice President of the
International Diabetes Federation.


     Mr. Rumsfeld is currently Chairman of the Board of Directors of Gilead
Sciences, Inc. He also serves as a member of the boards of directors of Asea
Brown Boveri Ltd., Tribune Company and RAND Corporation. He is currently
Chairman of the Salomon Smith Barney International Advisory Board and a member
of the Forstmann Little & Co. Advisory Board. From 1991 to 1996, Mr. Rumsfeld
served as a member of the board of directors of Amylin Pharmaceuticals. Mr.
Rumsfeld was Chairman and Chief Executive Officer of General Instrument
Corporation from October 1990 to August 1993 and served as a senior advisor to
William Blair & Co., an investment banking firm, from 1985 to 1990. He was Chief
Executive Officer of G.D. Searle & Co. from 1977 to 1985. Mr. Rumsfeld formerly
served as U.S. Secretary of Defense, White House Chief of Staff, U.S. Ambassador
to NATO, and U.S. congressman. He has also served as the President's special
envoy to the Middle East. He is a recipient of the Presidential Medal of
Freedom, the United States' highest civilian award.



CORPORATE INFORMATION


     We were incorporated in Delaware in September 1987. Our executive offices
are currently located at 9373 Towne Centre Drive, San Diego, California 92121,
and our telephone number is (858) 552-2200.

     SYMLIN is our trademark. All other brand names or trademarks appearing in
this prospectus are the property of their respective holders.

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<PAGE>   7

                                  RISK FACTORS


     Except for the historical information contained or incorporated by
reference, this prospectus (and the information incorporated by reference)
contains forward-looking statements that involve risks and uncertainties. Our
actual results could differ materially from those discussed here or incorporated
by reference. Factors that could cause or contribute to differences in our
actual results include those discussed in the following section, as well as
those discussed elsewhere in this prospectus and in any other documents
incorporated by reference into this prospectus.


     Investment in Amylin shares involves a high degree of risk. You should
consider the following discussion of risks as well as other information in this
prospectus before purchasing any Amylin shares. Each of these risk factors could
adversely affect our business, operating results and financial condition, as
well as adversely affect the value of an investment in our common stock.


RESULTS FROM OUR CLINICAL TRIALS MAY NOT BE SUFFICIENT TO OBTAIN REGULATORY
CLEARANCE TO MARKET SYMLIN OR AC2993 IN THE UNITED STATES OR ABROAD ON A TIMELY
BASIS, OR AT ALL.



     Clinical testing is a long, expensive and uncertain process. The data
collected from our clinical trials may not be sufficient to support approval of
SYMLIN or AC2993 by the United States Food and Drug Administration or any
foreign regulatory authorities. Moreover, preclinical and clinical data can be
interpreted in different ways, which could delay, limit or prevent regulatory
approval. Consequently, even if Amylin believes that preclinical and clinical
data are sufficient to support regulatory approval for SYMLIN or AC2993, the FDA
and foreign regulatory authorities may not ultimately approve those products for
commercial sale in any jurisdiction. If SYMLIN does not meet applicable
regulatory requirements for approval, we may not have the financial resources to
continue research and development of SYMLIN or any of our other product
candidates and we may not be able to generate revenues from the commercial sale
of any of our products.



DELAYS IN THE CONDUCT OR COMPLETION OF OUR CLINICAL TRIALS OR THE ANALYSIS OF
THE DATA FROM OUR CLINICAL TRIALS MAY RESULT IN DELAYS IN OUR PLANNED FILINGS
FOR REGULATORY APPROVALS, OR ADVERSELY AFFECT OUR ABILITY TO ENTER INTO NEW
COLLABORATIVE ARRANGEMENTS.



     Although we believe the data from our clinical studies for SYMLIN and
AC2993 obtained to date warrant continuing with development of these product
candidates, we cannot predict whether we will encounter problems with any of our
completed or ongoing clinical studies that will cause us or regulatory
authorities to delay or suspend our ongoing clinical studies or delay the
analysis of data from our completed or ongoing clinical studies. If the results
of our ongoing and planned clinical studies for SYMLIN and AC2993 are not
available when we expect or if we encounter any delay in the analysis of our
clinical studies:



     - we may delay the submission of our applications for regulatory approval
       of SYMLIN with regulatory authorities in North America and Europe,
       currently scheduled for mid-2000;



     - we may not have the financial resources to continue research and
       development of any of our product candidates; and



     - we may not be able to enter into collaborative arrangements relating to
       any product subject to delay in regulatory filing.



     Any of the following reasons could delay the completion of our ongoing and
future clinical studies:



     - delays in enrolling volunteers;



     - lower than anticipated retention rate of volunteers in a trial; or



     - serious adverse events relating to the product candidate.


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OUR FAILURE TO COMPLY WITH EXTENSIVE REGULATIONS ENFORCED BY DOMESTIC AND
FOREIGN REGULATORY AUTHORITIES COULD PREVENT OR DELAY THE COMMERCIALIZATION OF
OUR PRODUCT CANDIDATES.



     Our product candidates are subject to extensive government regulations
related to development, clinical trials, manufacturing and commercialization.
The process of obtaining FDA and other regulatory approvals is costly, time
consuming, uncertain and subject to unanticipated delays.



     The FDA may refuse to approve an application if it believes that applicable
regulatory criteria are not satisfied. The FDA may also require additional
testing for safety and efficacy. Moreover, if the FDA grants regulatory approval
of a product, the approval may be limited to specific indications or limited
with respect to its distribution. Foreign regulatory authorities may apply
similar limitations or may refuse to grant any approval.



     The FDA may not approve the SYMLIN clinical trials or manufacturing
processes. Manufacturing facilities operated by the third party manufacturers
with whom Amylin has contracted for the manufacture of SYMLIN may not pass an
FDA preapproval inspection for SYMLIN. Any failure to obtain or delay these
approvals could prohibit or delay us from marketing SYMLIN.



     Even if we are able to obtain United States regulatory approval for SYMLIN,
the approval will be subject to continual review, and newly discovered or
developed safety issues may result in revocation of the marketing approval.
Moreover, if and when we obtain marketing approval for SYMLIN, the marketing of
the product will be subject to extensive regulatory requirements administered by
the FDA and other regulatory bodies, including adverse event reporting
requirements and the FDA's general prohibition against promoting products for
unapproved or "off-label" uses. The SYMLIN manufacturing facilities are also
subject to continual review and periodic inspection and approval of
manufacturing modifications. Domestic manufacturing facilities are subject to
biennial inspections by the FDA and must comply with the FDA's Good
Manufacturing Practices regulations. In complying with these regulations,
manufacturers must spend funds, time and effort in the areas of production,
record keeping, personnel and quality control to ensure full technical
compliance. The FDA stringently applies regulatory standards for manufacturing.
Failure to comply with any of these postapproval requirements can, among other
things, result in warning letters, product seizures, recalls, fines,
injunctions, suspensions or revocations of marketing licenses, operating
restrictions and criminal prosecutions. Any of these enforcement actions or any
unanticipated changes in existing regulatory requirements or the adoption of new
requirements could adversely affect our ability to market products and generate
revenues and thus adversely affect our ability to continue as a going concern.



     Amylin and the manufacturers of SYMLIN also are subject to numerous
federal, state and local laws relating to such matters as safe working
conditions, manufacturing practices, environmental protection, fire hazard
control and hazardous substance disposal. In the future, we may incur
significant costs to comply with those laws and regulations.



PRICING REGULATIONS AND REIMBURSEMENT LIMITATIONS MAY PREVENT THE SALE OF OUR
PRODUCTS AT SATISFACTORY PRICES.



     The requirements governing product licensing, pricing and reimbursement
vary widely from country to country. Some countries require approval of the sale
price of a drug before it can be marketed. In many countries, the pricing review
period begins after product licensing approval is granted. As a result, we or
our partners may obtain regulatory approval for a product in a particular
country, but then be subject to price regulation that prevents the sale of the
product at satisfactory prices.



     Our ability to commercialize our products successfully also will depend in
part on the extent to which reimbursement for the cost of our products and
related treatments will be available from government health administration
authorities, private health insurers and other organizations. The


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<PAGE>   9


levels of revenues and profitability of pharmaceutical companies may be affected
by the continuing efforts of governmental and third-party payors to contain or
reduce the costs of health care through various means. For example, in some
foreign markets pricing or profitability of prescription pharmaceuticals is
subject to government control. In the United States, there have been, and we
expect that there will continue to be, a number of federal and state proposals
to implement similar government control. In addition, both in the United States
and elsewhere, sales of prescription pharmaceuticals are dependent in part on
the availability of reimbursement from third-party payors, such as government
and private insurance plans. Third-party payors are increasingly challenging the
prices charged for medical products and services. If we succeed in bringing
SYMLIN and/or AC2993 to the market, we cannot assure you that either product
will be considered cost effective and that reimbursement will be available or
will be sufficient to allow us to sell SYMLIN and/or AC2993 on a competitive
basis.



WE WILL REQUIRE FUTURE CAPITAL AND ARE UNCERTAIN OF THE AVAILABILITY OR TERMS OF
ADDITIONAL FUNDING. IF FUNDING BECOMES UNAVAILABLE, IS INADEQUATE, OR IS NOT
AVAILABLE ON ACCEPTABLE TERMS, IT MAY ADVERSELY EFFECT THE VALUE OF YOUR SHARES.



     We must continue to find sources of capital in order to complete the
development and commercialization of SYMLIN and AC2993. In 1999, we have
generated additional working capital through the private offering of $15 million
of preferred stock, which converted to common stock, and $18.5 million of common
stock, and the sale of assets of our Cabrillo Laboratories division. Our future
capital requirements will depend on many factors, including:



     - our ability to establish one or more development and/or commercialization
       collaborations for our SYMLIN and AC2993 programs;



     - progress with our preclinical studies and clinical studies;


     - the time and costs involved in obtaining regulatory approvals;


     - scientific progress in our other research programs and the magnitude of
       these programs;


     - the costs involved in preparing, filing, prosecuting, maintaining, and
       enforcing patents or defending ourselves against competing technological
       and market developments;


     - the costs of manufacturing SYMLIN and AC2993; and


     - the potential need to repay outstanding indebtedness.


     We anticipate that our existing cash, including interest income from cash
investments, will be adequate to satisfy our capital requirements into the
fourth quarter of 2000. We believe that we should be able to raise additional
funds through other corporate partnerships, equity offerings, debt offerings
and/or investor partnerships in order to fund our business following the fourth
quarter of 2000. However, you should be aware that:



     - we may not obtain additional financial resources in the necessary time
       frame or on terms favorable to us, if at all;



     - any available additional financing may not be adequate; and



     - we may be required to use future financing to repay existing indebtedness
       to our current or future creditors, including Johnson & Johnson.



     In the event we are unable to obtain additional financing on acceptable
terms, we would not have the financial resources to continue research and
development of SYMLIN, AC2993 or any of our other product candidates and we
would curtail or cease our operations, which would adversely effect the value of
your shares.


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<PAGE>   10


WE HAVE A HISTORY OF OPERATING LOSSES, ANTICIPATE FUTURE LOSSES, MAY NOT
GENERATE REVENUES FROM PRODUCT SALES AND MAY NEVER BECOME PROFITABLE.



     We have experienced significant operating losses since our inception in
1987. As of September 30, 1999, we had an accumulated deficit of approximately
$281 million. We expect to incur significant additional operating losses over
the next several years. We have derived substantially all of our revenues to
date from development funding, fees and milestone payments under collaborative
agreements and from interest income. To date, we have not received any revenues
from product sales. To achieve profitable operations, we, alone or with others,
must successfully develop, manufacture, obtain required regulatory approvals and
market our products. We may not ever become profitable. If we become profitable,
we may not remain profitable.



WE HAVE NO EXPERIENCE IN SALES, MARKETING AND DISTRIBUTION AND OUR ABILITY TO
ENTER INTO COLLABORATIVE ARRANGEMENTS OR OTHER THIRD PARTY RELATIONSHIPS IS
IMPORTANT TO OUR SUCCESSFUL DEVELOPMENT AND COMMERCIALIZATION OF PRODUCTS AND
POTENTIAL PROFITABILITY.



     We have limited experience in market development and no experience in
sales, marketing or distribution. To market any of our products directly, we
must obtain access to marketing and sales forces with technical expertise and
with supporting distribution capability. As a consequence, we believe that we
will likely need to find a corporate partner who can provide primary
responsibility for commercialization of SYMLIN and/or AC2993. We may not be able
to find a corporate partner for SYMLIN or AC2993. Moreover, any new corporate
partner for SYMLIN or AC2993 may not establish adequate sales and distribution
capabilities or gain market acceptance for products, if any.



OUR COMMERCIALIZATION PLANS FOR SYMLIN AND AC2993 ARE DEPENDENT ON THE
PERFORMANCE OF, AND OUR RELATIONSHIPS WITH, THIRD PARTIES THAT PROVIDE US WITH
PRODUCT DEVELOPMENT, MARKETING AND MANUFACTURING SUPPLIES AND SERVICES.



     From June 1995 to August 1998, Amylin and Johnson & Johnson collaborated on
the development and commercialization of SYMLIN pursuant to a worldwide
collaboration agreement to develop and commercialize pramlintide. After Johnson
& Johnson's termination of our earlier collaboration, we assumed full
responsibility for product development, marketing and manufacturing functions
for SYMLIN that were previously managed by Johnson & Johnson. In order for us to
perform those functions, we require the services of third-party providers of
product development and marketing services and manufacturers. While we believe
that business relations between us and our third-party suppliers and service
providers have been good, we cannot predict whether third-party suppliers and
service providers will continue to cooperate with us in the performance of our
most important services or functions. Any difficulties or interruptions of
service with our third-party suppliers and service providers could disrupt the
completion of our clinical trials, the manufacture of our products and delay our
filing for regulatory approval of SYMLIN.



WE DO NOT MANUFACTURE OUR OWN PRODUCTS AND MAY NOT BE ABLE TO OBTAIN ADEQUATE
SUPPLIES, WHICH COULD CAUSE DELAYS OR REDUCE PROFIT MARGINS.



     The manufacturing of sufficient quantities of new drugs is a time consuming
and complex process. We currently have no facilities for the manufacture of
clinical study or commercial supplies of SYMLIN or AC2993. We currently rely on
third parties to manufacture SYMLIN and AC2993 for preclinical testing and
clinical studies. We work with contract suppliers who have the capabilities for
the commercial manufacture of SYMLIN. All manufacturing facilities must comply
with applicable regulations of the FDA. We, alone or together with a new
corporate partner, may not be able to make the transition to commercial
production. We have established a quality control and quality assurance program,
including a set of standard operating procedures and specifications, designed to
ensure that our products are manufactured in accordance with the FDA's current
Good

                                        9
<PAGE>   11


Manufacturing Practices and other applicable domestic and foreign regulatory
standards. However, we are dependent upon contract manufacturers to comply
reliably with those procedures and regulations. While we believe that our
business relations between us and our contract manufacturers are good, we cannot
predict whether these manufacturers will meet our requirements for quality,
quantity or timeliness for the manufacture of SYMLIN or AC2993. Therefore, we
may not be able to obtain supplies of products on acceptable terms or in
sufficient quantities, if at all. Our dependence on third parties for the
manufacture of products may also reduce our profit margins and ability to
develop and deliver products with sufficient speed.



     If any of our existing manufacturers cease to manufacture SYMLIN, we may
need to locate and engage another manufacturer. The cost and time to establish
manufacturing facilities to produce SYMLIN would be substantial. As a result,
using a new manufacturer could delay bringing SYMLIN to market, disrupt our
ability to supply SYMLIN or reduce our profit margins. Any delay or disruption
in the manufacturing of SYMLIN could require us to raise additional funds.



OUR OTHER RESEARCH AND DEVELOPMENT PROGRAMS MAY NOT RESULT IN ADDITIONAL DRUG
CANDIDATES.



     Our research and development programs other than SYMLIN and AC2993 are at
an early stage. Any additional product candidates will require significant
research, development, preclinical and clinical testing, regulatory approval and
commitments of resources before commercialization. We cannot predict whether our
research will lead to the discovery of any additional product candidates.



WE EXPERIENCE A SUBSTANTIAL DEGREE OF UNCERTAINTY RELATING TO PATENTS THAT, IF
DETERMINED TO BE UNENFORCEABLE, COULD RESULT IN THE LOSS OF THE PATENT OR CLAIMS
AGAINST US.



     We own or hold exclusive rights to 28 issued United States patents and
approximately 30 pending United States patent applications. Of these issued
patents and patent applications, we have a total of 11 issued U.S. patents and
nine pending applications that we believe are relevant to the development and
commercialization of SYMLIN and one issued US patent and seven pending
applications that we believe are relevant to the development and
commercialization of AC2993. We also own or hold exclusive rights to various
foreign patent applications that correspond to issued United States patents or
pending United States patent applications.


     Our success will depend in part on our ability to (1) obtain patent
protection for our products and technologies both in the United States and other
countries and (2) operate without infringing the proprietary rights of third
parties. Legal standards relating to the validity of patents covering
pharmaceutical and biotechnological inventions and the scope of claims made
under these patents are still developing. As a result, our ability to obtain and
enforce patents that protect our products is uncertain and involves complex
legal and factual questions.


     We cannot guarantee that any patents will issue from any pending or future
patent applications owned by or licensed to us. Third parties may challenge or
infringe upon existing or future patents. In the event that a third party
challenges a patent, a court may invalidate the patent or determine that the
patent is not enforceable. Alternatively, a third party may successfully
circumvent our patents. Our rights under any issued patents may not provide us
with sufficient protection against competitive products or otherwise cover
commercially valuable products or processes. Because patent applications in the
United States are maintained in secrecy until patents issue and publication of
discoveries in the scientific or patent literature often lag behind actual
discoveries, we cannot be sure that the inventors of subject matter covered by
our patents and patent applications were the first to invent or the first to
file patent applications for these inventions. In the event that a third party
has also filed a patent for any of its inventions, we may have to participate in
interference proceedings declared by the US Patent and Trademark Office to
determine priority of invention, which could result in substantial


                                       10
<PAGE>   12


cost to us, even if the eventual outcome is favorable to us. Furthermore, we may
not have identified all United States and foreign patents that pose a risk of
infringement.



LITIGATION REGARDING PATENTS AND OTHER PROPRIETARY RIGHTS MAY BE EXPENSIVE AND
CAUSE DELAYS IN BRINGING PRODUCTS TO MARKET.


Proceedings involving our patents or patent applications could result in adverse
decisions about:


     - the patentability of our inventions and products relating to SYMLIN and
       AC2993; and/or



     - the enforceability, validity or scope of protection offered by our
       patents relating to SYMLIN and AC2993.



     The manufacture, use or sale of SYMLIN or AC2993 may infringe on the patent
rights of others. If we are unable to avoid infringement of the patent rights of
others, we may be required to seek a license, defend an infringement action or
challenge the validity of the patents in court. Patent litigation is costly and
time consuming. We may not have sufficient resources to bring these actions to a
successful conclusion. In addition, if we do not obtain a license, develop or
obtain non-infringing technology, and fail successfully to defend an
infringement action or to have infringing patents declared invalid, we may:


     - incur substantial money damages;


     - encounter significant delays in bringing SYMLIN or AC2993 to market;
       and/or



     - be precluded from participating in the manufacture, use or sale of SYMLIN
       or AC2993 or methods of treatment requiring licenses.



CONFIDENTIALITY AGREEMENTS WITH EMPLOYEES AND OTHERS MAY NOT ADEQUATELY PREVENT
DISCLOSURE OF TRADE SECRETS AND OTHER PROPRIETARY INFORMATION.



     In order to protect our proprietary technology and processes, we also rely
in part on confidentiality agreements with our corporate partners, employees,
consultants, outside scientific collaborators and sponsored researchers and
other advisors. These agreements may not effectively prevent disclosure of
confidential information and may not provide an adequate remedy in the event of
unauthorized disclosure of confidential information. In addition, others may
independently discover trade secrets and proprietary information. Costly and
time-consuming litigation could be necessary to enforce and determine the scope
of our proprietary rights, and failure to obtain or maintain trade secret
protection could adversely affect our competitive business position.



COMPETITION IN THE BIOTECHNOLOGY AND PHARMACEUTICAL INDUSTRIES MAY RESULT IN
COMPETING PRODUCTS, SUPERIOR MARKETING OF OTHER PRODUCTS AND LOWER REVENUES OR
PROFITS FOR US.


     We believe that competition may be intense for all of our product
candidates. Our competitors include multinational pharmaceutical and chemical
companies, specialized biotechnology firms and universities and other research
institutions. A number of our competitors are pursuing the development of novel
pharmaceuticals which target the same diseases that we are targeting, and we
expect that the number of companies seeking to develop products and therapies
for the treatment of diabetes and other metabolic disorders will increase. Many
of our competitors have substantially greater financial, technical and human
resources than we do. In addition, many of these competitors have significantly
greater experience than we do in undertaking preclinical testing and human
clinical studies of new pharmaceutical products and in obtaining regulatory
approvals of human therapeutic products. Accordingly, our competitors may
succeed in obtaining FDA approval for products more rapidly than we do.
Furthermore, if we are permitted to commence commercial sales of products, we
may also be competing with respect to manufacturing efficiency and marketing
capabilities, areas in which we have limited or no experience.

                                       11
<PAGE>   13

     Our target patient population for SYMLIN is people with diabetes whose
therapy includes multiple insulin injections daily. AC2993 is currently being
studied for the treatment of type 2 diabetes. Other products are currently in
development or exist in the market that may compete directly with the products
that we are seeking to develop and market. Various products are available to
treat type 2 diabetes, including:


<TABLE>
  <S>                           <C>
  - sulfonylureas               - repaglinide
  - metformin                   - alpha-glucosidase inhibitors
  - insulin                     - thiozolidinediones
</TABLE>



     In addition, several companies are developing various approaches to improve
treatments for type 1 and type 2 diabetes. We cannot predict whether our
products, even if successfully tested and developed, will have sufficient
advantages over existing products to cause health care professionals to adopt
them over other products or that our products will offer an economically
feasible alternative to existing products.



WE MAY NOT BE ABLE TO KEEP UP WITH THE RAPID TECHNOLOGICAL CHANGE IN THE
BIOTECHNOLOGY AND PHARMACEUTICAL INDUSTRIES, WHICH COULD MAKE OUR PRODUCTS
OBSOLETE.


     Biotechnology and related pharmaceutical technologies have undergone and
continue to be subject to rapid and significant change. We expect that the
technologies associated with biotechnology research and development will
continue to develop rapidly. Our future will depend in large part on our ability
to maintain a competitive position with respect to these technologies. Any
compounds, products or processes that we develop may become obsolete before we
recover expenses incurred in developing those products.


OUR FUTURE SUCCESS DEPENDS ON OUR ABILITY TO RETAIN OUR CHIEF EXECUTIVE OFFICER
AND OUR SENIOR VICE PRESIDENT OF CLINICAL AFFAIRS AND TO ATTRACT, RETAIN AND
MOTIVATE QUALIFIED PERSONNEL.



     We are highly dependent on Joseph C. Cook, Jr., our Chief Executive
Officer, and Orville G. Kolterman, M.D., our Senior Vice President of Clinical
Affairs, and the other principal members of our scientific and management staff,
the loss of whose services might impede the achievement of our research and
development objectives. Recruiting and retaining qualified scientific personnel
to perform research and development work in the future will also be critical to
our success. Although we believe we will be successful in attracting and
retaining skilled and experienced scientific personnel, we may not be able to
attract and retain these personnel on acceptable terms given the competition
between numerous pharmaceutical and biotechnology companies, universities and
other research institutions for experienced scientists and management personnel.
We do not maintain "key person" insurance on any of our employees. In addition,
we rely on consultants and advisors, including scientific and clinical advisors,
to assist us in formulating research and development strategy. Our consultants
and advisors may be employed by employers other than us and may have commitments
to or consulting or advisory contracts with other entities that may limit their
availability to us.



OUR BUSINESS HAS A SUBSTANTIAL RISK OF PRODUCT LIABILITY CLAIMS, AND INSURANCE
MAY BE EXPENSIVE OR UNAVAILABLE.


     Our business exposes us to potential product liability risks that are
inherent in the testing, manufacturing and marketing of human therapeutic
products. Product liability claims could result in a recall of products or a
change in the indications for which they may be used. Although we currently have
product liability insurance, we cannot assure you that insurance will provide
adequate coverage against potential liabilities. Furthermore, product liability
insurance is becoming increasingly expensive. As a result, we may not be able to
maintain current amounts of insurance coverage, obtain additional insurance or
obtain insurance at a reasonable cost or in sufficient amounts to protect
against losses that could have a material adverse effect on us.

                                       12
<PAGE>   14


OUR ACTIVITIES INVOLVE THE USE OF HAZARDOUS MATERIALS, WHICH SUBJECT US TO
REGULATION, RELATED COSTS AND DELAYS AND POTENTIAL LIABILITIES.


     Our research and development involves the controlled use of hazardous
materials, chemicals and various radioactive compounds. Although we believe that
our 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 eliminated. If
an accident occurs, we could be held liable for resulting damages, which could
be substantial. We are also subject to numerous environmental, health and
workplace safety laws and regulations, including those governing laboratory
procedures, exposure to blood-borne pathogens and the handling of biohazardous
materials. Additional federal, state and local laws and regulations affecting
our operations may be adopted in the future. We may incur substantial costs to
comply with and substantial fines or penalties if we violate any of these laws
or regulations.


PROVISIONS IN AMYLIN'S CORPORATE CHARTER AND BYLAWS MAY DISCOURAGE TAKE-OVER
ATTEMPTS AND THUS DEPRESS THE MARKET PRICE OF OUR STOCK.



     Provisions in Amylin's certificate of incorporation, as amended, may have
the effect of delaying or preventing a change of control or changes in its
management. These provisions include:



     - the right of the board of directors to elect a director to fill a vacancy
       created by the expansion of the board of directors; and



     - the ability of the board of directors to issue, without stockholder
       approval, up to 7,375,000 shares of preferred stock with terms set by the
       board of directors.



     Each of these provisions could discourage potential take-over attempts and
could adversely affect the market price of our common stock.



SUBSTANTIAL FUTURE SALES OF OUR COMMON STOCK COULD CAUSE OUR STOCK PRICE TO
FALL.



     Sales of a large number of shares of our common stock in the public market
after this offering or the perception that additional sales could occur could
cause the market price of our common stock to drop. As of November 12, 1999, we
had approximately 53.8 million shares of common stock outstanding. Sales of
common stock by existing stockholders in the public market, or the availability
of shares of our common stock for sale, could adversely affect the market price
of our common stock. Likewise, additional equity financings or other share
issuances by us, including shares issued in connection with strategic alliances,
could adversely affect the market price of our common stock.



SIGNIFICANT VOLATILITY IN THE MARKET PRICE FOR OUR COMMON STOCK COULD EXPOSE US
TO LITIGATION RISK.



     The market prices for securities of biopharmaceutical and biotechnology
companies, including our common stock, have historically been highly volatile,
and the market from time to time has experienced significant price and volume
fluctuations that are unrelated to the operating performance of these
biopharmaceutical and biotechnology companies. Given the uncertainty of our
future funding and our planned filing for regulatory approval of SYMLIN, we
expect that we may continue to experience volatility of our stock price during
the remainder of 1999 and throughout 2000. In addition, the following factors
may have a significant effect on the market price of our common stock:


     - announcements of additional clinical study results;

     - developments in our relationships with current or future collaborative
       partners;


     - fluctuations in our operating results;


     - public concern as to the safety of drugs developed by us;

     - technological innovations or new commercial therapeutic products by us or
       our competitors;

                                       13
<PAGE>   15

     - developments in patent or other proprietary rights;

     - governmental policy or regulation; and

     - general market conditions.


     Broad market and industry factors may materially adversely affect the
market price of our common stock, regardless of our actual operating
performance. In the past, following periods of volatility in the market price of
a company's securities, securities class-action litigation has often been
instituted against such companies. This type of litigation, if instituted, could
result in substantial costs and a diversion of management's attention and
resources, which would materially adversely affect our business, financial
condition and results of operations.



THE DELISTING OF OUR STOCK COULD MAKE TRADING OUR STOCK DIFFICULT AND CAUSE OUR
STOCK PRICE TO FALL.



     Our common stock was listed on the Nasdaq National Market from our initial
public offering through January 31, 1999. Since February 1, 1999, our common
stock has been listed for trading on the Nasdaq SmallCap Market. If our stock
price does not meet the $1.00 minimum requirements for listing on Nasdaq
SmallCap, Nasdaq may delist our securities from that market or we may be
required to effect a reverse stock split in order to maintain our listing.
Between December 1, 1998 and November 22, 1999 the market price of our common
stock has ranged from $0.375 per share to $9.625 per share. While the closing
price of our stock has been above $1.00 per share since April 20, 1999, if in
the future the market price of our common stock were to fall below $1.00 per
share we may not be able to maintain the listing of our common stock on Nasdaq
SmallCap or any other exchange. In the event that our common stock is delisted
from the Nasdaq SmallCap Market, our stock may be difficult to trade which could
also reduce the market price of our common stock. While we plan to reapply for
the listing of our common stock on the Nasdaq National Market, Nasdaq may not
approve our application.



YEAR 2000 ISSUES MAY RESULT IN UNANTICIPATED COSTS OR ADVERSE EFFECTS ON OUR
OPERATIONS.


     As is true for most companies, the Year 2000 problem creates a risk for
Amylin. If systems do not correctly recognize date information when the year
changes to 2000, there could be an adverse impact on our operations.


     We have reviewed our program for identifying and solving Year 2000 related
issues. This program involved the review and assessment of our internal
information technology and appropriate corrective action where necessary.



     We also have contacted our important business partners in order to assess
their progress in addressing Year 2000 issues. Information provided by them has
been used to assess their commitment to Year 2000 readiness. Based on the
information provided, we believe that our business partners are taking adequate
steps to ensure that their business operations will not be seriously disrupted
by Year 2000 issues. Additionally, our primary computer systems do not interface
directly with those of third parties, thus providing Amylin with further
confidence that our internal operations will not be disrupted even if third
parties fail to adequately complete their Year 2000 programs. However, in the
event that our third party business partners delay their own remediation efforts
or a third party cannot supply us with products or services, our results of
operations could be adversely affected. Similarly, if significant new
non-compliance issues are identified, our business operations could be
materially adversely affected. For example, our research and development efforts
could be interrupted, resulting in delays in the progress of our products,
including SYMLIN.


     Our most significant potential exposure to Year 2000 problems is related to
our dependence on commercial utilities. If our water and power supply were
interrupted, our research and development activities as well as our general
business operations would be seriously affected until services could be

                                       14
<PAGE>   16


restored or until suitable alternate sources could be secured. Amylin has
limited back-up diesel power generation capability. In the event of a power
outage, Amylin could operate for approximately 24 hours before needing to
refuel. We have received reasonable assurances from local diesel suppliers that
additional fuel will be available if needed and therefore Amylin has decided not
to stockpile diesel fuel. We have an adequate water supply to operate for 30
days, if necessary.



     Year 2000 costs to date have been primarily related to internal personnel
costs and external consulting costs. Total external costs to remediate Year 2000
problems are estimated at less than $100,000. At this time, we have no reason to
believe that Year 2000 issues will have a material impact on our business or
financial condition.



                      WHERE YOU CAN FIND MORE INFORMATION



     We file annual, quarterly and special reports, proxy statements and other
information with the SEC. You may read and copy the documents we file at the
SEC's public reference rooms in Washington, D.C., New York, New York and
Chicago, Illinois. You can request copies of these documents by writing to the
SEC and paying a fee for the copying cost. Please call the SEC at 1-800-SEC-0330
for further information on the public reference rooms. Our SEC filings are also
available to the public at no cost from the SEC's website at http://www.sec.gov.



     We incorporate by reference the documents listed below, except as
superseded or modified by this registration statement, and any future filings we
will make with the SEC under Sections 13(a), 13(c), 14 or 15(d) of the
Securities and Exchange Act of 1934:



     1. Annual report on Form 10-K for the fiscal year ended December 31, 1998;



     2. Quarterly reports on Form 10-Q for the quarters ended March 31, 1999,
June 30, 1999 and September 30, 1999; and



     3. Notice of Annual Meeting and Proxy Statement for annual meeting of
stockholders held on May 24, 1999.



     You may request a copy of these filings at no cost, by writing or
telephoning us at the following address:



       Investor Relations
        Amylin Pharmaceuticals, Inc.
        9373 Towne Centre Drive
        San Diego, California 92121
        Telephone: (858) 552-2200


                                       15
<PAGE>   17


                DISCLOSURE REGARDING FORWARD-LOOKING STATEMENTS



     This prospectus, including the documents that we incorporate by reference,
contains forward-looking statements within the meaning of Section 27A of the
Securities Act and Section 21E of the Exchange Act. Any statements about our
expectations, beliefs, plans, objectives, assumptions or future events or
performance are not historical facts and may be forward-looking. These
statements are often, but not always, made through the use of words or phrases
such as "anticipate," "estimate," "plans," "projects," "continuing," "ongoing,"
"expects," "management believes," "the Company believes," "the Company intends,"
"we believe," "we intend" and similar words or phrases. Accordingly, these
statements involve estimates, assumptions and uncertainties which could cause
actual results to differ materially from those expressed in them. Any
forward-looking statements are qualified in their entirety by reference to the
factors discussed throughout this prospectus. Among the key factors that could
cause actual results to differ materially from the forward-looking statements:



     - scientific and technological uncertainties regarding our product
       candidates;



     - risks and uncertainties regarding the adequacy of our clinical trial
       processes and whether the results of those clinical trials will be
       adequate to support regulatory filings and/or approvals;



     - our ability to raise additional needed capital or consummate strategic or
       corporate partner transactions on favorable terms or at all;



     - risks associated with timing of filing for regulatory approval of SYMLIN,
       and if regulatory approval is received, time to market thereafter; and



     - dependence on third party service providers and manufacturers of our
       products.



     Because the risk factors referred to above, as well as the risk factors
beginning on page 6 of this prospectus, could cause actual results or outcomes
to differ materially from those expressed in any forward-looking statements made
by us or on behalf of the Company, you should not place undue reliance on any of
those forward-looking statements. Further, any forward-looking statement speaks
only as of the date on which it is made, and we undertake no obligation to
update any forward-looking statement to reflect events or circumstances after
the date on which the statement is made or to reflect the occurrence of
unanticipated events. New factors emerge from time to time, and it is not
possible for us to predict which factors will arise. In addition, we cannot
assess the impact of each factor on our business or the extent to which any
factor, or combination of factors, may cause actual results to differ materially
from those contained in any forward-looking statements.


                                       16
<PAGE>   18

                                SECURITY HOLDERS


     We are registering for resale certain shares of Amylin common stock held by
the security holders identified below. The following table sets forth:



     - the name of the security holders,



     - the number and percent of shares of Amylin common stock that the security
       holders beneficially owned prior to the offering for resale of any of the
       shares of Amylin common stock being registered by this registration
       statement,



     - the number of shares of Amylin common stock that may be offered for
       resale for the account of the security holders pursuant to this
       prospectus, and



     - the number and percent of shares of Amylin common stock to be held by the
       security holders after the offering of the resale shares (assuming all of
       the resale shares are sold by the security holders).



     This table is prepared based on information supplied to us by the listed
security holders, schedules 13G and Forms 3 and 4, and other public documents
filed with the SEC, and assumes the sale of all of the resale shares. The
applicable percentages of ownership are based on an aggregate of 49,958,838
shares of Amylin common stock issued and outstanding on September 2, 1999,
adjusted as required by rules promulgated by the SEC.



<TABLE>
<CAPTION>
                                         SHARES BENEFICIALLY                  SHARES BENEFICIALLY
                                                OWNED             NUMBER             OWNED
                                          PRIOR TO OFFERING      OF SHARES       AFTER OFFERING
                                        ----------------------     BEING     ----------------------
           SECURITY HOLDERS              NUMBER     PERCENT(3)    OFFERED     NUMBER     PERCENT(3)
           ----------------             ---------   ----------   ---------   ---------   ----------
<S>                                     <C>         <C>          <C>         <C>         <C>
Allen Andersson(1)....................  6,920,459      13.9%     5,205,559   1,714,900      3.4%
Susan Riecken(2)......................  6,920,459      13.9%     5,205,559   1,714,900      3.4%
Funds Managed by Domain Associates,
  LLC(3)..............................  5,708,716      11.4%     5,037,605     671,111      1.3%
Charles A. Dunn Jr. and Sharon G.
  Dunn, Co-Trustees UTD 5/5/81........    209,866         *        209,866           0        *
Vaughn D. Bryson(4)...................     52,013         *         42,013      10,000        *
Donald H. Rumsfeld(5).................     95,027         *         84,027      11,000        *
Rumsfeld Family Trust.................     83,926         *         83,926           0        *
VMN Associates........................     83,926         *         83,926           0        *
Kingsbury Capital Partners, L.P.
  III.................................  1,259,401       2.5%     1,259,401           0        *
The Greene Family Trust(6)............  2,083,352       4.2%       335,806   1,747,546      3.5%
Joseph C. Cook, Jr.(7)................  1,868,490       3.7%       251,880   1,616,610      3.2%
</TABLE>


- -------------------------
 *  less than 1%


(1) This amount includes 2,602,729 shares held by Susan Riecken, Mr. Andersson's
    spouse.



(2) This amount includes 4,317,730 shares held by Allen Andersson, Ms. Riecken's
    spouse.



(3) Includes 4,919,726 shares held by Domain Partners IV, L.P., 117,879 shares
    held by DP IV Associates, L.P., 653,847 shares held by Domain Partners II,
    L.P., and 17,264 shares which Mr. James C. Blair has the right to acquire
    within 60 days after the date of this table pursuant to outstanding options.
    Mr. Blair is a member of the Board of Directors of Amylin and also is a
    general partner of One Palmer Square Associates II, L.P., and a managing
    member of One Palmer Square Associates IV, LLC. One Palmer Square Associates
    II, L.P. is the general partner of Domain Partners II, L.P. One Palmer
    Square Associates IV, LLC is the general partner of Domain Partners IV, L.P.
    and DP IV Associates, L.P.


                                       17
<PAGE>   19


(4) Includes 10,000 shares held by the Vaughn D. Bryson Irrevocable Trust, U-A
    1/14/99. Mr. Bryson is a director of Amylin.



(5) Includes 10,000 shares which Mr. Rumsfeld has the right to acquire within 60
    days after the date of this table pursuant to outstanding options.



(6) This amount includes 45,769 shares held by The Greene Children's Trust, of
    which Howard E. Greene, Jr. is trustee, and 7,264 shares which Mr. Greene
    has the right to acquire within 60 days after the date of this table
    pursuant to outstanding options. Mr. Greene is the trustee of The Greene
    Family Trust and is also a member of Amylin's Board of Directors.



(7) Includes 100,752 shares held of record by Farview Management Co., L.P. and
    151,128 shares held of record by Judith E. and Joseph C. Cook, Jr. Also
    includes 40,000 and 827,024 shares which Farview Management Co., L.P. and
    Mr. Cook, respectively, have the right to acquire within 60 days after the
    date of this table pursuant to outstanding options. Mr. Cook has served as
    the Chief Executive Officer and Chairman of the Board of Amylin since March
    1998, and as a director since November 1994, and is also a partner of
    Farview Management, Co., L.P.


                                       18
<PAGE>   20

                              PLAN OF DISTRIBUTION


     The resale shares may be sold from time to time by the security holders in
one or more transactions at:



     - fixed prices,



     - market prices at the time of sale,



     - varying prices determined at the time of sale, or



     - negotiated prices.



The security holders may offer their resale shares in one or more of the
following transactions:



     - on any national securities exchange or quotation service on which the
       Amylin common stock may be listed or quoted at the time of sale,
       including the Nasdaq SmallCap Market;



     - in the over-the-counter market;



     - in private transactions;



     - through options;



     - by pledge to secure debts or other obligations; or



     - a combination of any of the above transactions.



     The security holders may effect these transactions by selling to or through
one or more broker-dealers, and broker-dealers involved in these transactions
may receive compensation in the form of underwriting discounts, concessions or
commissions from the security holders. The security holders and any
broker-dealers that participate in the distribution may, under certain
circumstances, be deemed to be "underwriters" within the meaning of the
Securities Act, and any commissions received by those broker-dealers and any
profits realized on any resale of the resale shares by them might be deemed to
be underwriting discounts and commissions under the Securities Act.



     Under applicable rules and regulations under the Exchange Act, any person
engaged in the distribution of the resale shares may not simultaneously engage
in market making activities with respect to Amylin's common stock for a period
of two business days prior to the commencement of such distribution. In addition
and without limiting the foregoing, the security holders and any other person
participating in a distribution will be subject to applicable provisions of the
Exchange Act and the rules and regulations thereunder, including without
limitation, Regulation M under the Exchange Act, which may limit the timing of
purchases and sales of shares of Amylin common stock by the security holders or
any such other person.



     We will make copies of this prospectus available to the security holders
and have informed the security holders of the need for delivery of a copy of
this prospectus to each purchaser of the resale shares prior to or at the time
of any sale of the resale shares.



     The security holders will pay all underwriting discounts, commissions,
transfer taxes and other expenses associated with the sale of the resale shares
by them. We will pay all costs and expenses associated with the registration of
the resale shares. We estimate that our expenses in connection with this
offering will be approximately $102,583.


                                       19
<PAGE>   21

                                USE OF PROCEEDS


     We will not receive any of the proceeds from the sale of any of the resale
shares by the security holders. All proceeds from the sale of the resale shares
will be for the accounts of the security holders.


                                 LEGAL MATTERS


     Cooley Godward LLP, San Diego, California will pass upon the validity of
the issuance of the common stock offered by this prospectus.


                                    EXPERTS


     The consolidated financial statements of Amylin Pharmaceuticals, Inc. at
December 31, 1998 and 1997, and for each of the three years in the period ended
December 31, 1998, appearing in this prospectus and registration statement have
been audited by Ernst & Young LLP, independent auditors, as set forth in their
report appearing elsewhere here in, and are included in reliance upon such
report given on the authority of such firm as experts in accounting and
auditing.


                                       20
<PAGE>   22

                   INDEX TO CONSOLIDATED FINANCIAL STATEMENTS

<TABLE>
<CAPTION>
                                                              PAGE
                                                              ----
<S>                                                           <C>
Report of Ernst & Young LLP, Independent Auditors...........  F-2
Consolidated Balance Sheets as of December 31, 1998 and
  1997......................................................  F-3
Consolidated Statements of Operations for the years ended
  December 31, 1998, 1997 and 1996..........................  F-4
Consolidated Statement of Stockholders' Equity (Net Capital
  Deficiency) for the years ended December 31, 1998, 1997
  and 1996..................................................  F-5
Consolidated Statements of Cash Flows for the years ended
  December 31, 1998, 1997 and 1996..........................  F-6
Notes to Consolidated Financial Statements..................  F-7
</TABLE>

                                       F-1
<PAGE>   23

               REPORT OF ERNST & YOUNG LLP, INDEPENDENT AUDITORS

The Board of Directors and Stockholders
Amylin Pharmaceuticals, Inc.

     We have audited the accompanying consolidated balance sheets of Amylin
Pharmaceuticals, Inc. as of December 31, 1998 and 1997, and the related
consolidated statements of operations, stockholders' equity (net capital
deficiency), and cash flows for each of the three years in the period ended
December 31, 1998. 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 in accordance with generally accepted auditing
standards. Those standards 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. An audit also includes
assessing the accounting principles used and significant estimates made by
management, as well as evaluating the overall financial statement presentation.
We believe that our audits provide a reasonable basis for our opinion.

     Since the date of completion of our audit of the accompanying financial
statements and initial issuance of our report thereon dated March 12, 1999,
except for Note 7, as to which the date is March 23, 1999, as discussed in Note
1, the Company's estimated available cash and short-term investments are
expected to last only into the first quarter of 2000. Note 1 includes
management's discussion of this issue.

     In our opinion, the financial statements referred to above present fairly,
in all material respects, the consolidated financial position of Amylin
Pharmaceuticals, Inc. at December 31, 1998 and 1997, and the consolidated
results of its operations and its cash flows for each of the three years in the
period ended December 31, 1998, in conformity with generally accepted accounting
principles.

                                          ERNST & YOUNG LLP

San Diego, California
March 12, 1999,
except for Note 7 as to which the date is
March 23, 1999
and the last paragraph of Note 1, as to which the date is
September 9, 1999

                                       F-2
<PAGE>   24

                          AMYLIN PHARMACEUTICALS, INC.

                          CONSOLIDATED BALANCE SHEETS

                                     ASSETS

<TABLE>
<CAPTION>
                                                                     DECEMBER 31,
                                                             -----------------------------
                                                                 1998            1997
                                                             -------------   -------------
<S>                                                          <C>             <C>
Current assets:
  Cash and cash equivalents................................  $   8,787,000   $  46,903,000
  Short-term investments...................................      2,002,000       5,845,000
  Receivable from related party............................             --         966,000
  Other current assets.....................................        514,000       1,298,000
                                                             -------------   -------------
Total current assets.......................................     11,303,000      55,012,000
Property and equipment, at cost:
  Equipment................................................     15,197,000      14,707,000
  Leasehold improvements...................................      3,955,000       4,763,000
                                                             -------------   -------------
                                                                19,152,000      19,470,000
  Less accumulated depreciation and amortization...........    (13,556,000)    (10,860,000)
                                                             -------------   -------------
                                                                 5,596,000       8,610,000
Patents, net...............................................      1,779,000       1,664,000
Other assets at cost.......................................        145,000          52,000
                                                             -------------   -------------
                                                             $  18,823,000   $  65,338,000
                                                             =============   =============

              LIABILITIES AND STOCKHOLDERS' EQUITY (NET CAPITAL DEFICIENCY)
Current liabilities:
  Accounts payable.........................................  $   2,187,000   $   5,278,000
  Accrued liabilities, including other deferred revenue....      2,130,000      10,606,000
  Deferred collaborative revenue from related party........             --       6,357,000
  Current portion of notes payable to unrelated parties....      1,794,000       1,240,000
  Current portion of obligations under capital leases......             --         228,000
                                                             -------------   -------------
Total current liabilities..................................      6,111,000      23,709,000
  Notes payable............................................      4,164,000       3,047,000
Note payable to related party..............................     39,925,000      33,933,000
Other long-term obligations................................         85,000              --
Commitments and contingencies
Stockholders' equity (net capital deficiency):
  Preferred stock, $.001 par value, 7,500,000 shares
     authorized, none issued and outstanding...............             --              --
  Common stock, $.001 par value, 100,000,000 shares
     authorized, 36,726,000 and 32,394,000 issued and
     outstanding at December 31, 1998 and 1997,
     respectively..........................................         37,000          33,000
  Additional paid-in capital...............................    229,757,000     215,245,000
  Accumulated deficit......................................   (260,830,000)   (209,732,000)
  Deferred compensation....................................       (428,000)       (893,000)
  Accumulated other comprehensive income...................          2,000          (4,000)
                                                             -------------   -------------
Total stockholders' equity (net capital deficiency)........    (31,462,000)      4,649,000
                                                             -------------   -------------
                                                             $  18,823,000   $  65,338,000
                                                             =============   =============
</TABLE>

                            See accompanying notes.
                                       F-3
<PAGE>   25

                          AMYLIN PHARMACEUTICALS, INC.

                     CONSOLIDATED STATEMENTS OF OPERATIONS

<TABLE>
<CAPTION>
                                                        YEARS ENDED DECEMBER 31,
                                              --------------------------------------------
                                                  1998            1997            1996
                                              ------------    ------------    ------------
<S>                                           <C>             <C>             <C>
Revenues under collaborative agreements with
related party...............................  $ 16,236,000    $ 42,609,000    $ 35,803,000
Expenses:
  Research and development..................    53,597,000      82,281,000      64,998,000
  General and administrative................    10,191,000      15,592,000      10,420,000
                                              ------------    ------------    ------------
                                                63,788,000      97,873,000      75,418,000
                                              ------------    ------------    ------------
Loss from operations........................   (47,552,000)    (55,264,000)    (39,615,000)
Interest and other income...................     1,424,000       2,613,000       2,274,000
Interest and other expense..................    (4,970,000)     (1,976,000)       (446,000)
                                              ------------    ------------    ------------
Net loss....................................  $(51,098,000)   $(54,627,000)   $(37,787,000)
                                              ============    ============    ============
Basic and diluted net loss per share........  $      (1.49)   $      (1.70)   $      (1.31)
                                              ============    ============    ============
Shares used in computing net loss per
  share -- basic and diluted................    34,325,326      32,155,761      28,744,822
                                              ============    ============    ============
</TABLE>

                            See accompanying notes.
                                       F-4
<PAGE>   26

                          AMYLIN PHARMACEUTICALS, INC.

                 CONSOLIDATED STATEMENT OF STOCKHOLDERS' EQUITY
                            (NET CAPITAL DEFICIENCY)
       FOR EACH OF THE THREE YEARS IN THE PERIOD ENDED DECEMBER 31, 1998

<TABLE>
<CAPTION>
                                                                                                     ACCUMULATED
                                   COMMON STOCK        ADDITIONAL                                       OTHER           TOTAL
                               --------------------     PAID-IN       ACCUMULATED      DEFERRED     COMPREHENSIVE   STOCKHOLDERS'
                                 SHARES     AMOUNT      CAPITAL         DEFICIT      COMPENSATION      INCOME          EQUITY
                               ----------   -------   ------------   -------------   ------------   -------------   -------------
<S>                            <C>          <C>       <C>            <C>             <C>            <C>             <C>
Balance at December 31,
  1995.......................  28,018,000   $28,000   $166,994,000   $(117,318,000)  $        --      $ 50,000        49,754,000
Comprehensive income (loss):
    Net loss.................          --       --              --     (37,787,000)           --            --       (37,787,000)
    Unrealized loss on
      available-for-sale
      securities.............          --       --              --              --            --       (66,000)          (66,000)
                                                                                                                    ------------
    Comprehensive loss.......          --       --              --              --            --            --       (37,853,000)
    Issuance of common stock
      in public offering.....   2,012,000    2,000      18,767,000              --            --            --        18,769,000
    Issuance of common stock
      in private placement...   1,500,000    1,000      14,999,000              --            --            --        15,000,000
    Issuance of common stock
      upon exercise of
      options................     447,000    1,000       1,967,000              --            --            --         1,968,000
    Deferred compensation
      related to stock
      options................          --       --       2,073,000              --    (2,073,000)           --                --
    Amortization of deferred
      compensation...........          --       --              --              --       896,000            --           896,000
                               ----------   -------   ------------   -------------   -----------      --------      ------------
Balance at December 31,
  1996.......................  31,977,000   32,000     204,800,000    (155,105,000)   (1,177,000)      (16,000)       48,534,000
  Comprehensive income
    (loss):
    Net loss.................          --       --              --     (54,627,000)           --            --       (54,627,000)
    Unrealized gain on
      available-for-sale
      securities.............          --       --              --              --            --        12,000            12,000
                                                                                                                    ------------
    Comprehensive loss.......          --       --              --              --            --            --       (54,615,000)
    Issuance of common stock
      upon exercise of
      options................     417,000    1,000       2,100,000              --            --            --         2,101,000
    Deferred compensation
      related to stock
      options................          --       --         261,000              --      (261,000)           --                --
    Amortization of deferred
      compensation...........          --       --              --              --       545,000            --           545,000
    Discount on Note Payable
      related to grant of
      common stock
      warrants...............          --       --       8,084,000              --            --            --         8,084,000
                               ----------   -------   ------------   -------------   -----------      --------      ------------
Balance at December 31,
  1997.......................  32,394,000   33,000     215,245,000    (209,732,000)     (893,000)       (4,000)        4,649,000
  Comprehensive income
    (loss):
    Net loss.................          --       --              --     (51,098,000)           --            --       (51,098,000)
    Unrealized loss on
      available-for-sale
      securities.............          --       --              --              --            --         6,000             6,000
                                                                                                                    ------------
    Comprehensive loss.......          --       --              --              --            --            --       (51,092,000)
    Issuance of common stock
      upon exercise of
      options................     130,000      130         549,000              --            --            --           549,000
    Issuance of common stock
      for employer 401(k)
      match..................      81,000       81         458,000              --            --            --           458,000
    Issuance of common stock
      in private placement...   4,000,000    4,000      12,730,000              --            --            --        12,734,000
    Issuance of common stock
      under Employee Stock
      Purchase Plan..........     121,000      121         438,000              --            --            --           438,000
    Deferred compensation
      related to stock
      options................          --       --         337,000              --      (337,000)           --                --
    Amortization of deferred
      compensation...........          --       --              --              --       802,000            --           802,000
                               ----------   -------   ------------   -------------   -----------      --------      ------------
Balance at December 31,
  1998.......................  36,726,000   $37,000   $229,757,000   $(260,830,000)  $  (428,000)     $  2,000      $(31,462,000)
                               ==========   =======   ============   =============   ===========      ========      ============
</TABLE>

                            See accompanying notes.

                                       F-5
<PAGE>   27

                          AMYLIN PHARMACEUTICALS, INC.

                     CONSOLIDATED STATEMENTS OF CASH FLOWS

<TABLE>
<CAPTION>
                                                           YEARS ENDED DECEMBER 31,
                                                  ------------------------------------------
                                                      1998           1997           1996
                                                  ------------   ------------   ------------
<S>                                               <C>            <C>            <C>
OPERATING ACTIVITIES:
Net loss........................................  $(51,098,000)  $(54,627,000)  $(37,787,000)
Adjustments to reconcile net loss to net cash
  used in operating activities:
  Depreciation and amortization.................     2,696,000      2,865,000      2,345,000
  Deferred revenue from related party...........    (6,357,000)    (1,597,000)     3,336,000
  Deferred rent and other expense...............            --        (17,000)       (25,000)
  Amortization of deferred compensation.........       802,000        545,000        896,000
  Amortization of warrants issued with debt.....     1,198,000        299,000             --
  Changes in operating assets and liabilities:
  Receivable from related party.................       966,000      1,123,000     (1,866,000)
  Other current assets..........................       784,000       (156,000)       130,000
  Accounts payable..............................    (3,091,000)       449,000      3,352,000
  Accrued liabilities...........................    (8,711,000)     5,995,000      1,750,000
                                                  ------------   ------------   ------------
Net cash flows used in operating activities.....   (62,811,000)   (45,121,000)   (27,869,000)
INVESTING ACTIVITIES:
Purchases of short-term investments.............    (2,158,000)   (15,541,000)   (38,972,000)
Maturities of short-term investments............     2,000,000     19,005,000     29,642,000
Sales of short-term investments.................     3,995,000     10,172,000     26,607,000
Sale (purchase) of equipment and leasehold
  improvements..................................       318,000     (4,641,000)    (3,278,000)
Increase in deposits, patents and other
  assets........................................       122,000       (371,000)      (313,000)
                                                  ------------   ------------   ------------
Net cash flows provided by investing
  activities....................................     4,277,000      8,624,000     13,686,000
FINANCING ACTIVITIES:
Issuance of notes payable.......................     7,707,000     40,467,000      5,379,000
Principal payments on capital leases and
  equipment notes payable.......................    (1,468,000)    (1,822,000)      (988,000)
Issuance of common stock, net...................    14,179,000      2,101,000     35,737,000
                                                  ------------   ------------   ------------
Net cash flows provided by financing
  activities....................................    20,418,000     40,746,000     40,128,000
                                                  ------------   ------------   ------------
Decrease in cash and cash equivalents...........   (38,116,000)     4,249,000     25,945,000
Cash and cash equivalents at beginning of
  period........................................    46,903,000     42,654,000     16,709,000
                                                  ------------   ------------   ------------
Cash and cash equivalents at end of period......  $  8,787,000   $ 46,903,000   $ 42,654,000
                                                  ============   ============   ============
SUPPLEMENTAL DISCLOSURES OF CASH FLOW
  INFORMATION:
Interest paid...................................  $    129,000   $    411,000   $    281,000
                                                  ============   ============   ============
</TABLE>

                            See accompanying notes.

                                       F-6
<PAGE>   28

                          AMYLIN PHARMACEUTICALS, INC.

                   NOTES TO CONSOLIDATED FINANCIAL STATEMENTS

 1. SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES

  ORGANIZATION AND BUSINESS ACTIVITY

     Amylin Pharmaceuticals, Inc. ("Amylin" or the "Company") was incorporated
in Delaware on September 29, 1987. The Company is an early development
pharmaceutical company focused on metabolic disorders, and specializing in
preclinical characterization of lead molecules and demonstration of proof of
principle in humans. The Company is conducting a series of Phase 3 clinical
trials of its leading drug candidate, pramlintide, in people with type 1 or
insulin-using type 2 diabetes. The Company is also conducting clinical trials of
AC2993 (synthetic exendin-4), a second diabetes drug candidate.

  PRINCIPLES OF CONSOLIDATION

     The consolidated financial statements include the accounts of the Company
and its wholly owned subsidiary, Amylin Europe Limited. All significant
intercompany transactions and balances have been eliminated in consolidation.

  RESEARCH REVENUES UNDER COLLABORATIVE AGREEMENTS AND RESEARCH AND DEVELOPMENT
EXPENSES

     Research revenues under collaborative agreements are recorded when earned
as research activities are performed. Payments in excess of amounts earned are
deferred. Research and development costs are expensed as incurred.

  CASH, CASH EQUIVALENTS AND SHORT-TERM INVESTMENTS

     Cash, cash equivalents and short-term investments consist principally of
U.S. government securities and other highly liquid debt instruments. The Company
considers instruments with remaining maturities of less than 90 days when
purchased to be cash equivalents.

  CONCENTRATION OF CREDIT RISK

     The Company invests its excess cash in U.S. government securities and debt
instruments of financial institutions and corporations with strong credit
ratings. The Company has established guidelines relative to diversification and
maturities that maintain safety and liquidity. These guidelines are periodically
reviewed.

  INVESTMENTS

     The Company has classified its debt securities as available-for-sale, and
accordingly, carries its short term investments at fair value, and unrealized
holding gains or losses on these securities are carried as a separate component
of stockholders' equity. The amortized cost of debt securities in this category
is adjusted for amortization of premiums and accretion of discounts to maturity.
Such amortization is included in interest income. Realized gains and losses and
declines in value judged to be other-than-temporary (of which there have been
none to date) on available-for-sale securities are included in interest income.
The cost of securities sold is based on the specific identification method.

  DEPRECIATION AND AMORTIZATION

     Depreciation of equipment is computed using the straight-line method over
two to five years. Leasehold improvements are amortized over the shorter of the
estimated useful lives of the assets or

                                       F-7
<PAGE>   29
                          AMYLIN PHARMACEUTICALS, INC.

             NOTES TO CONSOLIDATED FINANCIAL STATEMENTS (CONTINUED)

the remaining term of the lease. Amortization of equipment under capital leases
is reported with depreciation of property and equipment. Patents consist of
patent filing costs which are amortized over the estimated economic life of the
patents when issued.

  NET LOSS PER SHARE

     In 1997, the Financial Accounting Standards Board issued Statement of
Financial Accounting Standard ("SFAS") No. 128, Earnings per Share. SFAS 128
replaced the calculation of primary and fully diluted earnings per share with
basic and diluted earnings per share. Unlike primary earnings per share, basic
earnings per share excludes any dilutive effects of options, warrants and
convertible securities. Diluted earnings per share is very similar to the
previously reported fully diluted earnings per share. The adoption of SFAS 128
had no effect on the Company's financial statements.

  OPTIONS

     The Company has elected to follow Accounting Principles Board Opinion No.
25 Accounting for Stock Issued to Employees and related Interpretations ("APB
25") in accounting for its employee stock options. Under APB 25, when the
exercise price of the Company's employee stock options is not less than the
market price of the underlying stock on the date of grant, no compensation
expense is recognized.

  COMPREHENSIVE INCOME

     Effective January 1, 1998, the Company adopted SFAS No. 130, Reporting
Comprehensive Income, which requires that all components of comprehensive
income, including net income, be reported in the financial statements in the
period in which they are recognized. Comprehensive income is defined as the
change in equity during a period from transactions and other events and
circumstances from non-owner sources. Net income and other comprehensive income,
including unrealized gains and losses on investments, shall be reported, net of
their related tax effect, to arrive at comprehensive income. Prior year
financial statements have been reclassified to conform to the requirements of
SFAS No. 130.

  USE OF 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 and liabilities and the
disclosure of contingent assets and liabilities at the date of the financial
statements and the reported amounts of revenues and expenses during the
reporting period. Actual results could differ from those estimates.

  LIQUIDITY


     The Company's future capital requirements will depend on many factors,
including the ability of the Company to establish one or more development and/or
commercialization collaborations for its SYMLIN program, the time and costs
involved in obtaining regulatory approvals, scientific progress in its
non-SYMLIN research and development programs, the cost involved in preparing,
filing, prosecuting, maintaining, enforcing or defending itself against patents,
competing technological and market developments, and the costs of manufacturing
scale-up. The Company anticipates that its


                                       F-8
<PAGE>   30
                          AMYLIN PHARMACEUTICALS, INC.

             NOTES TO CONSOLIDATED FINANCIAL STATEMENTS (CONTINUED)


existing cash including interest income from cash investments will be adequate
to satisfy the Company's capital requirements into the fourth quarter of 2000.
The Company believes that it should be able to raise additional funds through
other corporate partnerships, equity offerings, debt offerings and/or investor
partnerships. However, there can be no assurance that additional financial
resources will be raised in the necessary time frame or on terms favorable to
the Company if at all. In the event the Company is unable to obtain additional
financing on acceptable terms, the Company will not have the financial resources
to continue research and development of SYMLIN or any of the Company's other
product candidates.


 2. INVESTMENTS

     The following is a summary of investments as of December 31, 1998 and 1997,
including $7,628,000 and $37,211,000 classified as cash equivalents in the
accompanying balance sheets as of December 31, 1998 and 1997, respectively. All
respective investments mature in less than one year.

<TABLE>
<CAPTION>
                                                          AVAILABLE-FOR-SALE SECURITIES
                                                -------------------------------------------------
                                                               GROSS        GROSS
                                                             UNREALIZED   UNREALIZED   ESTIMATED
                                                   COST        GAINS        LOSSES     FAIR VALUE
                                                ----------   ----------   ----------   ----------
<S>                                             <C>          <C>          <C>          <C>
DECEMBER 31, 1998
U.S. Treasury securities and obligations of
U.S. government agencies......................  $5,051,000     $1,000        $--       $5,052,000
Other debt securities.........................   4,577,000      1,000         --        4,578,000
                                                ----------     ------        ---       ----------
          Total...............................  $9,628,000     $2,000        $--       $9,630,000
                                                ==========     ======        ===       ==========
</TABLE>

<TABLE>
<CAPTION>
                                                         AVAILABLE-FOR-SALE SECURITIES
                                              ---------------------------------------------------
                                                              GROSS        GROSS
                                                            UNREALIZED   UNREALIZED    ESTIMATED
                                                 COST         GAINS        LOSSES     FAIR VALUE
                                              -----------   ----------   ----------   -----------
<S>                                           <C>           <C>          <C>          <C>
DECEMBER 31, 1997
U.S. Treasury securities and obligations of
U.S. government agencies....................  $21,832,000      $--        $(3,000)    $21,829,000
Other debt securities.......................   21,228,000       --         (1,000)     21,227,000
                                              -----------      ---        -------     -----------
          Total.............................  $43,060,000      $--        $(4,000)    $43,056,000
                                              ===========      ===        =======     ===========
</TABLE>

     The gross realized gains on sales of available-for-sale securities totaled
$1,400 and $1,000 and the gross realized losses totaled $500 and $3,000 for the
years ended December 31, 1998 and 1997, respectively.

 3. COMMITMENTS

  LEASES

     The Company leases its facilities and certain machinery and equipment under
operating and capital leases. The minimum annual rent on the Company's
facilities is subject to increases based on stated rental adjustment terms of
certain leases, taxes, insurance and operating costs. Certain

                                       F-9
<PAGE>   31
                          AMYLIN PHARMACEUTICALS, INC.

             NOTES TO CONSOLIDATED FINANCIAL STATEMENTS (CONTINUED)

equipment leases require the Company to provide the lessor with a guaranteed
residual at the end of the lease term at which time title to the equipment
passes to the Company.

     Minimum future annual obligations for operating leases for years ending
after December 31, 1998 are as follows:

<TABLE>
<S>                                           <C>
1999........................................  $  926,000
2000........................................     827,000
2001........................................     860,000
2002........................................     894,000
Thereafter..................................   1,571,000
                                              ----------
          Total minimum lease payments......  $5,078,000
                                              ==========
</TABLE>

     Rent expense for 1998, 1997, and 1996 was $2,402,000, $2,697,000 and
$2,315,000, respectively.

  DEBT

     As of December 31, 1998, the Company had an outstanding loan of $15,000 for
financing of equipment and tenant improvements. The loan is payable over
forty-eight months which commenced on February 1, 1995. Payments include
principal and monthly interest of prime plus 1.75% (9.5% at December 31, 1998)
of the outstanding principal balance. The loan agreement contains provisions for
the complete repayment of any outstanding principal balance should the Company's
cash balances fall below certain minimum levels.

     In 1996, the Company entered into a master line of credit agreement (as
amended) to provide up to $5,000,000 of net financing for standard equipment. As
of December 31, 1998, the Company had an outstanding loan balance of $3,243,896.
Borrowings under each loan schedule are payable over forty-eight months to
include principal and monthly interest based on the average of three and five-
year U.S. Treasury maturities (approximately 10.63% at December 31, 1998).
Principal payments due in 1999 through 2002 are $1,239,820, $1,272,351,
$705,520, and $26,205, respectively. The credit agreement provides the lender
with a security interest in all equipment financed under the line.

     In November 1997, the Company entered into a commitment agreement to enter
into a financing agreement which will provide up to $2,700,000 of financing for
equipment purchases. As of December 31, 1998, the Company had an outstanding
loan balance of $2,700,000. Borrowings under this agreement are payable over a
sixty-month period with principal payments commencing on January 1, 1999.
Monthly interest payments are calculated based on prime plus 0.5% (approximately
8.25% at December 31, 1998) of the outstanding principal balance and commenced
with the outstanding balance in 1998. Principal payments due in 1999 through
2003 are $540,000 annually. The credit agreement provides the lender with a
security interest in all equipment financed under the agreement and requires
payment of a security deposit of 50% of the outstanding balance should the
Company's cash balances fall below $10,000,000.

 4. STOCKHOLDERS' EQUITY

  STOCK PURCHASE PLAN

     In November 1991, the Company adopted the Employee Stock Purchase Plan (the
"Purchase Plan"), under which 500,000 shares of common stock may be issued to
eligible employees, including officers. The price of common stock under the
Purchase Plan is equal to the lessor of 85% of the

                                      F-10
<PAGE>   32
                          AMYLIN PHARMACEUTICALS, INC.

             NOTES TO CONSOLIDATED FINANCIAL STATEMENTS (CONTINUED)

market price on the effective date of an employee's participation in the plan or
85% of the fair market value of the common stock at the purchase date. At
December 31, 1998, 422,956 shares of common stock had been issued under the
plan.

  STOCK OPTIONS

     Under the Company's 1991 Stock Option Plan (the "Plan"), 7,800,000 shares
of common stock are reserved for issuance upon exercise of options granted to
employees and consultants of the Company. The Plan provides for the grant of
incentive and nonstatutory stock options. The exercise price of incentive stock
options must equal at least the fair market value on the date of grant, and the
exercise price of nonstatutory stock options may be no less than 85% of the fair
market value on the date of grant. Additionally, the Company is authorized to
issue supplemental stock options for up to 70,000 options outside of the Plan.
The maximum term of all options granted is ten years.

     Under the Company's Non-Employee Directors' Stock Option Plan (the
"Directors' Plan") 350,000 shares of common stock are reserved for issuance upon
exercise of nonqualified stock options granted to Non-Employee Directors of the
Company.

     The following table summarizes option activity:

<TABLE>
<CAPTION>
                                                  SHARES         WEIGHTED
                                                  UNDER          AVERAGE
                                                  OPTION      EXERCISE PRICE
                                                ----------    --------------
<S>                                             <C>           <C>
Outstanding at December 31, 1995..............   4,308,233        $ 5.74
  Granted.....................................   1,927,796        $10.58
  Exercised...................................    (404,671)       $ 4.46
  Cancelled...................................    (331,576)       $ 9.43
                                                ----------        ------
Outstanding at December 31, 1996..............   5,499,782        $ 7.31
  Granted.....................................     566,914        $11.94
  Exercised...................................    (376,826)       $ 4.71
  Cancelled...................................    (327,231)       $ 8.48
                                                ----------        ------
Outstanding at December 31, 1997..............   5,362,639        $ 7.91
  Granted.....................................   3,364,337        $ 2.54
  Exercised...................................    (169,069)       $ 4.32
  Cancelled...................................  (2,590,778)       $ 8.67
                                                ----------        ------
Outstanding at December 31, 1998..............   5,967,129        $ 4.65
                                                ==========        ======
</TABLE>

     At December 31, 1998, 1,214,555 shares remained available for grant or
sale.

                                      F-11
<PAGE>   33
                          AMYLIN PHARMACEUTICALS, INC.

             NOTES TO CONSOLIDATED FINANCIAL STATEMENTS (CONTINUED)

     Following is a further breakdown of the options outstanding as of December
31, 1998:

<TABLE>
<CAPTION>
                                          WEIGHTED            WEIGHTED
                                          AVERAGE             AVERAGE                            WEIGHTED
        RANGE            NUMBER          REMAINING            EXERCISE          NUMBER       AVERAGE EXERCISE
 OF EXERCISE PRICES    OUTSTANDING    CONTRACTUAL LIFE         PRICE          EXERCISABLE         PRICE
 ------------------    -----------    ----------------    ----------------    -----------    ----------------
<S>                    <C>            <C>                 <C>                 <C>            <C>
$0.313                  1,230,000           9.81             $ 0.31300                --        $ 0.00000
$0.438 - $4.375         1,138,441           7.76               2.62945           438,166          2.31577
$4.500                  1,254,223           5.05               4.50000         1,254,038          4.50000
$4.750 - $7.125         1,288,041           7.19               5.81223           896,949          6.02831
$7.250 - $14.375        1,056,424           6.52              10.65456           966,715         10.51093
                        ---------           ----             ---------         ---------        ---------
$0.313 - $14.375        5,967,129           7.27             $ 4.65292         3,555,868        $ 6.25052
                        =========           ====             =========         =========        =========
</TABLE>

     Adjusted pro forma information regarding net loss and loss per share is
required by SFAS No. 123, and has been determined as if the Company had
accounted for its employee stock options and stock purchase plan under the fair
value method of SFAS No. 123. The fair value for these options was estimated at
the date of grant using the "Black-Scholes" method for option pricing with the
following weighted average assumptions for 1998, 1997 and 1996, respectively:
risk-free interest of 5.50%, 5.71% and 6.39%; dividend yield of 0%; volatility
factors of the expected market price of the Company's common stock of 73.5%,
65.4% and 64.7%; and a weighted-average expected life of the option of five
years.

     For purposes of adjusted pro forma disclosures, the estimated fair value of
the option is amortized to expense over the option's vesting period.

     The Company's adjusted pro forma information is as follows:

<TABLE>
<CAPTION>
                                                        YEAR ENDED DECEMBER 31,
                                              --------------------------------------------
                                                  1998            1997            1996
                                              ------------    ------------    ------------
<S>                                           <C>             <C>             <C>
Adjusted pro forma net loss.................  $(52,713,000)   $(59,850,000)   $(41,969,000)
Adjusted pro forma basic and diluted net
  loss per share............................  $      (1.54)   $      (1.86)   $      (1.46)
</TABLE>

     The weighted-average fair value of options granted during 1998, 1997, and
1996 was $1.66, $7.14 and $6.67, respectively.

  STOCK WARRANTS

     In May 1997, in conjunction with an amendment to a License Agreement, the
Company issued warrants to the licensor to purchase 20,000 shares of the
Company's common stock with a fixed exercise price of $11.375 per share and a
10-year exercise period.

     On September 30, 1997, in conjunction with the draw down under the
Development Loan Facility with Johnson & Johnson, the Company issued a warrant
to Johnson & Johnson to purchase 1,530,950 shares of the Company's common stock
at an exercise price of $12.00 per share which expires on September 29, 2007
(see "Collaborative Agreements").

                                      F-12
<PAGE>   34
                          AMYLIN PHARMACEUTICALS, INC.

             NOTES TO CONSOLIDATED FINANCIAL STATEMENTS (CONTINUED)

  SHARES RESERVED FOR FUTURE ISSUANCE

     The following shares of common stock are reserved for future issuance at
December 31, 1998:

<TABLE>
<S>                                                   <C>
1991 Stock Option Plan..............................   6,803,198
Employee Stock Purchase Plan........................      91,211
Directors Plan......................................     328,576
Phantom Stock Plan..................................     141,195
Warrants............................................   1,530,950
                                                      ----------
                                                       8,895,130
                                                      ==========
</TABLE>

 5. COLLABORATIVE AGREEMENTS

  JOHNSON & JOHNSON

     In June 1995, the Company entered into a worldwide Collaboration Agreement
(the "Collaboration Agreement") with LifeScan, Inc. for the development and
commercialization of pramlintide, a diabetes drug candidate currently in Phase 3
clinical trials. In conjunction with the Collaboration Agreement, the Company
also entered into a Stock Purchase Agreement with Johnson & Johnson Development
Corporation ("JJDC") and a Loan Agreement with Johnson & Johnson. LifeScan, Inc.
and JJDC, each of which are wholly-owned subsidiaries of Johnson & Johnson, are
referred to herein as Johnson & Johnson.

     Johnson & Johnson paid the Company a license fee, which was recognized as
revenue upon the signing of the Collaboration Agreement in 1995. Approximately
$16.2 million, $33.6 million, and $27.4 million of development payments were
made to the Company and recognized as revenues during 1998, 1997, and 1996,
respectively. Also included in receivables from related party was $1.0 million
of pre-marketing expenses due to the Company from Johnson & Johnson as of
December 31, 1997. Additionally, the Company's December 31, 1997 balance sheet
includes approximately $6.4 million in short-term deferred revenues reflecting
amounts advanced from Johnson & Johnson representing an equalization payment for
its share of projected development expenses for the first quarter of 1997.
Payments from Johnson & Johnson to Amylin Pharmaceuticals for development
expenses were recognized as revenue in the period in which they were earned.

     In accordance with the terms of the Stock Purchase Agreement, Johnson &
Johnson purchased 3,455,407 shares of the Company's common stock through
December 31, 1998.

     In September 1997, the Company received proceeds of approximately $30.6
million from the loan facility (the "Development Loan Facility"). The proceeds
were applied against the Company's one-half share of development expenses for
pramlintide. The loan carries an interest rate of 9.0%. In conjunction with the
borrowing, the Company issued warrants to Johnson & Johnson to purchase
1,530,950 shares of the Company's common stock over a 10-year exercise period.
The estimated fair value of the warrants has been accounted for as a discount
from the face value of the note. The loan is repayable beginning 12 months after
approval of a new drug application for pramlintide with 50% of the Company's
pramlintide profits, if any, subject to certain exceptions set forth in the
Development Loan facility. The loan is secured by the Company's issued patents
and patent applications relating to Amylin. Additionally, as of December 31,
1998, the Company owed Johnson & Johnson approximately $12.3 million for its
share of pre-launch marketing expenses.

                                      F-13
<PAGE>   35
                          AMYLIN PHARMACEUTICALS, INC.

             NOTES TO CONSOLIDATED FINANCIAL STATEMENTS (CONTINUED)

     In February 1998, Johnson & Johnson provided the Company with six-months
notice of its intention to terminate their collaboration. Johnson & Johnson's
financial and other obligations under the Collaboration Agreement continued
during the termination notice period and ended in August 1998. Based upon
Johnson & Johnson's decision, Amylin restructured its operations which included
reducing its workforce by approximately 25%. The impact of this restructuring
slowed down other (non-pramlintide) research programs.

     In September 1998, the Company entered into a repurchase agreement (the
"Pramlintide Repurchase Agreement") with Ortho-Biotech, Inc., an affiliate of
Johnson & Johnson ("J&J"), which provided that J&J will order and purchase
certain amounts of pramlintide from third party vendors and will place in
inventory such amounts of pramlintide for possible future purchase by Amylin.
J&J will purchase the pramlintide from certain vendors based upon agreed upon
prices per gram. The repurchase price of the compound shall be the same price
paid by J&J to the supplier. Amylin must repurchase the pramlintide in full on
the first to occur of the following: (i) Amylin executes any agreement with a
major company relating to the development, commercialization and/or sale of
pramlintide; (ii) Amylin requests in writing that J&J process the material or
requests that J&J transfer the material to a third party for processing; (iii)
Amylin receives regulatory approval for the sale of pramlintide; or (iv) Amylin
is acquired by a third party. If none of the above listed events occur, Amylin
will not have an obligation to purchase the pramlintide inventory from J&J. As
of December 31, 1998, J&J had purchased pramlintide inventory for Amylin
totaling approximately $1.1 million.

 6. INCOME TAXES

     Significant components of the Company's deferred tax assets as of December
31, 1998 and 1997 are shown below. A valuation allowance of $109,822,000, of
which $42,232,000 is related to 1998 changes, has been recognized as of December
31, 1998 to offset the deferred tax assets as realization of such assets is
uncertain.

<TABLE>
<CAPTION>
                                                1998             1997
                                            -------------    ------------
<S>                                         <C>              <C>
Deferred tax assets:
Capitalized research expenses.............  $   8,672,000    $  9,653,000
Net operating loss carryforwards..........     87,943,000      68,892,000
Research and development credits..........     12,464,000       9,615,000
Other.....................................        743,000       3,790,000
                                            -------------    ------------
Total deferred tax assets.................    109,822,000      91,950,000
Valuation allowance for deferred tax
  assets..................................   (109,822,000)    (91,950,000)
                                            -------------    ------------
Net deferred tax assets...................  $          --    $         --
                                            =============    ============
</TABLE>

     Approximately $382,000 of the valuation allowance for deferred tax assets
relates to stock option deductions which when recognized will be allocated
directly to additional paid-in capital.

     At December 31, 1998, the Company has federal, California and foreign tax
net operating loss carryforwards of approximately $241,881,000, $21,932,000 and
$6,528,000, respectively. The difference between the tax loss carryforwards for
federal and California purposes is attributable to the capitalization of
research and development expenses for California tax purposes and the fifty
percent limitation on California loss carryforwards. The federal tax loss
carryforwards will begin expiring in 2002 unless previously utilized. The
California tax loss carryforwards will continue to expire in 1999

                                      F-14
<PAGE>   36
                          AMYLIN PHARMACEUTICALS, INC.

             NOTES TO CONSOLIDATED FINANCIAL STATEMENTS (CONTINUED)

($998,000 expired in 1998). The Company also has federal and California research
and development tax credit carryforwards of $10,149,000 and $3,561,000,
respectively, which will begin expiring in 2003 unless previously utilized.

     Pursuant to Internal Revenue Code Sections 382 and 383, the use of the
Company's net operating loss and credit carryforwards may be limited if a
cumulative change in ownership of more than 50% occurs within a three-year
period. However, the Company does not believe that such a limitation would have
a material impact upon the future utilization of these carryforwards.


 7. SUBSEQUENT EVENTS


     In March 1999, the Company raised $15 million through a private placement
of Series A Convertible Preferred Stock (the "Series A Preferred Stock") to a
group of investors ("the Investors"). Subject to adjustment in certain events,
the Series A Preferred Stock is convertible into common stock of the Company at
$1.20 per share (the "Conversion Price"). The Conversion Price will be adjusted
using a weighted-average formula for issuances of other securities at a price
per share lower than the then current Conversion Price, provided that, at no
time shall the Conversion Price fall below $0.96 per share. The Series A
Preferred Stock accrues dividends at a rate of 5% of the purchase price per
share per annum. Beginning at the first anniversary of the closing, dividends
are payable semi-annually in cash or common stock valued at a ten day trailing
average closing price.


     On September 2, 1999, all of the outstanding shares of the Company's Series
A Preferred Stock automatically converted into an aggregate of 12,594,009 shares
of common stock.


                                      F-15
<PAGE>   37

                                    PART II

                     INFORMATION NOT REQUIRED IN PROSPECTUS

ITEM 14. OTHER EXPENSES OF ISSUANCE AND DISTRIBUTION.

     The following table sets forth all expenses payable by the Registrant in
connection with the sale of the common stock being registered. All the amounts
shown are estimates except for the registration fee.

<TABLE>
<S>                                                           <C>
SEC Registration Fee........................................  $ 12,583
Legal fees and expenses.....................................  $ 75,000
Transfer Agent's Fees.......................................  $  5,000
Accounting fees and expenses................................  $ 10,000
                                                              --------
  Total.....................................................  $102,583
                                                              ========
</TABLE>

ITEM 15. INDEMNIFICATION OF OFFICERS AND DIRECTORS.

     Under Section 145 of the Delaware General Corporation Law, the Registrant
has broad powers to indemnify its directors and officers against liabilities
they may incur in such capacities, including liabilities under the Securities
Act of 1933, as amended (the "Securities Act").

     The Registrants Certificate of Incorporation and By-laws include provisions
to (i) eliminate the personal liability of its directors for monetary damages
resulting from breaches of their fiduciary duty to the extent permitted by
Section 102(b)(7) of the General Corporation Law of Delaware (the "Delaware
Law") and (ii) require the Registrant to indemnify its Directors and officers to
the fullest extent permitted by Section 145 of the Delaware Law, including
circumstances in which indemnification is otherwise discretionary. Pursuant to
Section 145 of the Delaware Law, a corporation generally has the power to
indemnify its present and former directors, officers, employees and agents
against expenses incurred by them in connection with any suit to which they are
or are threatened to be made, a party by reason of their serving in such
positions so long as they acted in good faith and in a manner they reasonably
believed to be in or not opposed to, the best interests of the corporation and
with respect to any criminal action, they had no reasonable cause to believe
their conduct was unlawful. The Registrant believes that these provisions are
necessary to attract and retain qualified persons as directors and officers.
These provisions do not eliminate the directors' duty of care, and, in
appropriate circumstances, equitable remedies such as injunctive or other forms
of non-monetary relief will remain available under Delaware Law. In addition,
each director will continue to be subject to liability for breach of the
director's duty of loyalty to the Registrant, for acts or omissions not in good
faith or involving intentional misconduct, for knowing violations of law, for
acts or omissions that the director believes to be contrary to the best
interests of the Registrant or its stockholders, for any transaction from which
the director derived an improper personal benefit, for acts or omissions
involving a reckless disregard for the director's duty to the Registrant or its
stockholders when the director was aware or should have been aware of a risk of
serious injury to the Registrant or its stockholders, for acts or omissions that
constitute an unexcused pattern of inattention that amounts to an abdication of
the director's duty to the Registrant or its stockholders, for improper
transactions between the director and the Registrant and for improper
distributions to stockholders and loans to directors and officers. The provision
also does not affect a director's responsibilities under any other law, such as
the federal securities law or state or federal environmental laws.

     The Registrant has entered into indemnity agreements with each of its
directors and executive officers that require the Registrant to indemnify such
persons against expenses, judgments, fines, settlements and other amounts
incurred (including expenses of a derivative action) in connection with any
proceeding, whether actual or threatened, to which any such person may be made a
party by

                                      II-1
<PAGE>   38

reason of the fact that such person is or was a director or an executive officer
of the Registrant or any of its affiliated enterprises, such person acted in
good faith and in a manner such person reasonably believed to be in or not
opposed to the best interests of the Registrant and, with respect to any
criminal proceeding, had no reasonable cause to believe his conduct was
unlawful. The indemnification agreements also set forth certain procedures that
will apply in the event of a claim for indemnification thereunder.

     At present, there is no pending litigation or proceeding involving a
director or officer of the Registrant as to which indemnification is being
sought nor is the Registrant aware of any threatened litigation that may result
in claims for indemnification by any officer or director.

     The Registrant has an insurance policy covering the officers and directors
of the Registrant with respect to certain liabilities, including liabilities
arising under the Securities Act or otherwise.

ITEM 16. EXHIBITS

(a) Exhibits.


<TABLE>
<CAPTION>
    EXHIBIT
    NUMBER                       DESCRIPTION OF DOCUMENT
    -------                      -----------------------
    <C>        <S>
       3.1     Registrant's Amended and Restated Certificate of
               Incorporation.(1)
       3.2     Registrant's Amended and Restated Bylaws.(1)
       3.3     Registrant's Certificate of Amendment of Amended and
               Restated Certificate of Incorporation.(2)
       3.4     Certificate of Designation of the 5% Series A Convertible
               Preferred Stock of the Registrant.(3)
       3.5     Amendment to Registrant's Amended and Restated Bylaws.(4)
       4.1     Reference is made to Exhibits 3.1-3.4.
       4.2     Form of Stock Purchase Agreement dated March 22, 1999
               between the Registrant and purchasers of the Registrant's 5%
               Series A Convertible Preferred Stock.(3)
       5.1*    Opinion of Cooley Godward LLP.
      23.1     Consent of Ernst & Young LLP, Independent Auditors.
      23.3*    Consent of Cooley Godward LLP. Reference is made to Exhibit
               5.1.
</TABLE>


- -------------------------

  * Previously filed as an exhibit to this Registration Statement.



(1) Filed as an exhibit to Registrant's Registration Statement on Form S-1 (No.
    333-44195) or amendments thereto and incorporated herein by reference.



(2) Filed as an exhibit to Registrant's Registration Statement on Form S-3 (No.
    333-58831) or amendments thereto, and incorporated herein by reference.



(3) Filed as an exhibit to Registrant's Annual Report on form 10-K for the
    fiscal year ended December 31, 1998.



(4) Filed as an exhibit to Registrant's Quarterly Report on Form 10-Q for the
    quarter ended September 30, 1999.


ITEM 17. UNDERTAKINGS.

     Insofar as indemnification for liabilities arising under the Securities Act
of 1933 may be permitted to directors, officers, and controlling persons of the
Registrant pursuant to the provisions described in Item 15 or otherwise, the
Registrant has been advised that in the opinion of the SEC, such indemnification
is against public policy as expressed in the Act and is, therefore,
unenforceable. In the event that a claim for indemnification against such
liabilities (other than the payment by the Registrant of expenses incurred or
paid by a director, officer, or controlling person of the Registrant in
                                      II-2
<PAGE>   39

the successful defense of any action, suit, or proceeding) is asserted by such
director, officer, or controlling person in connection with the securities being
registered, the Registrant will, unless in the opinion of its counsel the matter
has been settled by controlling precedent, submit to a court of appropriate
jurisdiction the question whether such indemnification by it is against public
policy as expressed in the Act and will be governed by the final adjudication of
such issue.

     The undersigned Registrant hereby undertakes:

          (1) to file, during any period in which offers or sales are being
     made, a post-effective amendment to this registration statement:

             (i) to include any prospectus required by section 10(a)(3) of the
        Securities Act of 1933;

             (ii) to reflect in the prospectus any facts or events arising after
        the effective date of the registration statement (or the most recent
        post-effective amendment thereof) which, individually or in the
        aggregate, represent a fundamental change in the information set forth
        in the registration statement;

             (iii) to include any material information with respect to the plan
        of distribution not previously disclosed in the registration statement
        or any material change to such information in the registration
        statement;

     provided, however, that clauses (i) and (ii) do not apply if the
     information required to be included in a post-effective amendment by these
     clauses is contained in periodic reports filed by the Registrant pursuant
     to section 13 or section 15(d) of the Securities Exchange Act of 1934 that
     are incorporated by reference in the registration statement;

          (2) that, for the purpose of determining any liability under the
     Securities Act, each such post-effective amendment that contains a form of
     prospectus shall be deemed to be a new registration statement relating to
     the securities offered therein, and the offering of such securities at that
     time shall be deemed to be the initial bona fide offering thereof;

          (3) to remove from registration by means of a post-effective amendment
     any of the securities being registered which remain unsold at the
     termination of the offering; and

          (4) that, for purposes of determining any liability under the
     Securities Act of 1933, each filing of the Registrant's annual report
     pursuant to section 13(a) or section 15(d) of the Securities Exchange Act
     of 1934 (and, where applicable, each filing of an employee benefit plan's
     annual report pursuant to Section 15(d) of the Securities Exchange Act of
     1934) that is incorporated by reference in the registration statement shall
     be deemed to be a new registration statement relating to the securities
     offered therein, and the offering of such securities at that time shall be
     deemed to be the initial bona fide offering thereof.

                                      II-3
<PAGE>   40

                                   SIGNATURES


     Pursuant to the requirements of the Securities Act of 1933, the Registrant
certifies that it has reasonable grounds to believe that it meets all of the
requirements for filing on Form S-3 and has duly caused this Registration
Statement to be signed on its behalf by the undersigned, thereunto duly
authorized, in the City of San Diego, State of California, on the 23rd day of
November 1999.


                                          AMYLIN PHARMACEUTICALS, INC.

                                          By:      /s/ JOSEPH C. COOK
                                            ------------------------------------
                                                    Joseph C. Cook, Jr.
                                              Chairman of the Board and Chief
                                                     Executive Officer


     Pursuant to the requirements of the Securities Act of 1933, this
Registration Statement has been signed below by the following persons in the
capacities and on the dates indicated.



<TABLE>
<CAPTION>
                      SIGNATURE                                  TITLE                   DATE
                      ---------                                  -----                   ----
<C>                                                    <S>                        <C>
                 /s/ JOSEPH C. COOK                    Chairman of the Board and  November 23, 1999
- -----------------------------------------------------  Chief Executive Officer
                 Joseph C. Cook, Jr.

                 /s/ JAMES C. BLAIR*                   Director                   November 23, 1999
- -----------------------------------------------------
                   James C. Blair

                                                       Director                   November 23, 1999
- -----------------------------------------------------
                  Vaughn D. Bryson

                /s/ JAMES C. GAITHER*                  Director                   November 23, 1999
- -----------------------------------------------------
                  James C. Gaither

                /s/ GINGER L. GRAHAM*                  Director                   November 23, 1999
- -----------------------------------------------------
                  Ginger L. Graham

             /s/ HOWARD E. GREENE, JR.*                Director                   November 23, 1999
- -----------------------------------------------------
                Howard E. Greene, Jr.

               /s/ VAUGHN M. KAILIAN*                  Director                   November 23, 1999
- -----------------------------------------------------
                  Vaughn M. Kailian

                                                       Director                   November 23, 1999
- -----------------------------------------------------
                 Donald H. Rumsfeld

                                                       Director                   November 23, 1999
- -----------------------------------------------------
                 Jay S. Skyler, M.D.

                /s/ MARTIN R. BROWN*                   Vice President of          November 23, 1999
- -----------------------------------------------------  Operations (Principal
                   Martin R. Brown                     Accounting Officer)

*By: /s/ JOSEPH C. COOK, JR.
- -----------------------------------------------------
     Joseph C. Cook, Jr.
     Attorney-in-Fact
</TABLE>


                                      II-4
<PAGE>   41

                               INDEX TO EXHIBITS


<TABLE>
<CAPTION>
EXHIBIT
NUMBER                       DESCRIPTION OF DOCUMENT
- -------                      -----------------------
<C>        <S>
   3.1     Registrant's Amended and Restated Certificate of
           Incorporation.(1)
   3.2     Registrant's Amended and Restated Bylaws.(1)
   3.3     Registrant's Certificate of Amendment of Amended and
           Restated Certificate of Incorporation.(2)
   3.4     Certificate of Designation of the 5% Series A Convertible
           Preferred Stock of the Registrant.(3)
   3.5     Amendment to Registrant's Amended and Restated Bylaws.(4)
   4.1     Reference is made to Exhibits 3.1-3.4.
   4.2     Form of Stock Purchase Agreement dated March 23, 1999
           between the Registrant and purchasers of the Registrant's 5%
           Series A Convertible Preferred Stock.(3)
   5.1*    Opinion of Cooley Godward LLP.
  23.1     Consent of Ernst & Young LLP, Independent Auditors.
  23.3*    Consent of Cooley Godward LLP. Reference is made to Exhibit
           5.1.
</TABLE>


- -------------------------

  * Previously filed as an exhibit to this Registration Statement.



(1) Filed as an exhibit to Registrant's Registration Statement on Form S-1 (No.
    333-44195) or amendments thereto, and incorporated herein by reference.



(2) Filed as an exhibit to Registrant's Registration Statement on Form S-3 (No.
    333-58831) or amendments thereto, and incorporated herein by reference.



(3) Filed as an exhibit to Registrant's Annual Report on Form 10-K for the
    fiscal year ended December 31, 1998.



(4) Filed as an exhibit to Registrant's Quarterly Report on Form 10-Q for the
    quarter ended September 30, 1999.


<PAGE>   1
                                                                    EXHIBIT 23.1


               CONSENT OF ERNST & YOUNG LLP, INDEPENDENT AUDITORS


We consent to the reference to our firm under the caption "Experts" and to the
use of our report dated March 23, 1999 (except for Note 7, as to which the date
is March 23, 1999, and the last paragraph of Note 1, as to which the date is
September 9, 1999), in Amendment No. 1 to the Registration Statement (Form S-3
No. 333-87033) and related prospectus of Amylin Pharmaceuticals, Inc. for the
registration of 12,594,009 shares of its common stock.



                                                       ERNST & YOUNG LLP


San Diego, California
November 19, 1999



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