MILLENNIUM PHARMACEUTICALS INC
S-3, 2000-03-31
PHARMACEUTICAL PREPARATIONS
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<PAGE>
     AS FILED WITH THE SECURITIES AND EXCHANGE COMMISSION ON MARCH 31, 2000

                                            REGISTRATION STATEMENT NO. 333-
- --------------------------------------------------------------------------------
- --------------------------------------------------------------------------------

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

                                    FORM S-3
                             REGISTRATION STATEMENT

                                     UNDER

                           THE SECURITIES ACT OF 1933
                            ------------------------

                        MILLENNIUM PHARMACEUTICALS, INC.
             (Exact name of registrant as specified in its charter)

<TABLE>
<S>                                                        <C>
                     DELAWARE                                                  04-3177038
   (State or other jurisdiction of incorporation                            (I.R.S. Employer
                 or organization)                                          Identification No.)
</TABLE>

                                75 SIDNEY STREET
                         CAMBRIDGE, MASSACHUSETTS 02139
                                  617-679-7000
  (Address, including zip code, and telephone number, including area code, of
                   registrant's principal executive offices)
                         ------------------------------

                                 MARK J. LEVIN
                            CHIEF EXECUTIVE OFFICER
                        MILLENNIUM PHARMACEUTICALS, INC.
                                75 SIDNEY STREET
                         CAMBRIDGE, MASSACHUSETTS 02139
                                  617-679-7000
 (Name, address, including zip code, and telephone number, including area code,
                             of agent for service)
                         ------------------------------

                                   Copies to:

<TABLE>
<S>                                                           <C>
                   STEVEN D. SINGER, ESQ.                                      JOHN B. DOUGLAS III, ESQ.
                     HALE AND DORR LLP                                      MILLENNIUM PHARMACEUTICALS, INC.
                      60 STATE STREET                                               75 SIDNEY STREET
                BOSTON, MASSACHUSETTS 02109                                  CAMBRIDGE, MASSACHUSETTS 02139
                        617-526-6000                                                  617-679-7000
</TABLE>

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

    APPROXIMATE DATE OF COMMENCEMENT OF PROPOSED SALE TO PUBLIC: As soon as
practicable after this Registration Statement becomes effective.

    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>
<CAPTION>
                                                                              PROPOSED             PROPOSED
                                                                               MAXIMUM              MAXIMUM
                                                       AMOUNT TO BE        OFFERING PRICE          AGGREGATE
TITLE OF EACH CLASS OF SECURITIES TO BE REGISTERED     REGISTERED(1)        PER SHARE (2)      OFFERING PRICE(2)
<S>                                                 <C>                  <C>                  <C>
Common Stock, par value $.001 per share...                81,800               $146.44            $11,978,792

<CAPTION>

                                                         AMOUNT OF
TITLE OF EACH CLASS OF SECURITIES TO BE REGISTERED   REGISTRATION FEE
<S>                                                 <C>
Common Stock, par value $.001 per share...                $3,163
</TABLE>

(1) Pursuant to Rule 416 under the Securities Act, the amount to be registered
    also includes an indeterminate number of shares of common stock issuable as
    a result of stock splits and stock dividends.

(2) Estimated solely for purposes of calculating the amount of the registration
    fee pursuant to Rule 457(c) under the Securities Act and based upon the
    average of the high and low prices on the Nasdaq National Market on
    March 28, 2000.

    THE COMPANY HEREBY AMENDS THIS REGISTRATION STATEMENT ON SUCH DATE OR DATES
AS MAY BE NECESSARY TO DELAY ITS EFFECTIVE DATE UNTIL THE COMPANY SHALL FILE A
FURTHER AMENDMENT WHICH SPECIFICALLY STATES THAT THIS REGISTRATION STATEMENT
SHALL THEREAFTER BECOME EFFECTIVE IN ACCORDANCE WITH SECTION 8(A) OF THE
SECURITIES ACT OF 1933 OR UNTIL THE REGISTRATION STATEMENT SHALL BECOME
EFFECTIVE ON SUCH DATE AS THE COMMISSION, ACTING PURSUANT TO SAID SECTION 8(A),
SHALL DETERMINE.THE INFORMATION IN THIS PRELIMINARY PROSPECTUS IS NOT COMPLETE
AND MAY BE CHANGED. THESE SECURITIES MAY NOT BE SOLD UNTIL THE REGISTRATION
STATEMENT FILED WITH THE SECURITIES AND EXCHANGE COMMISSION IS EFFECTIVE. THIS
PRELIMINARY PROSPECTUS IS NOT AN OFFER TO SELL NOR DOES IT SEEK AN OFFER TO BUY
THESE SECURITIES IN ANY JURISDICTION WHERE THE OFFER OR SALE IS NOT PERMITTED.

- --------------------------------------------------------------------------------
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<PAGE>
                  SUBJECT TO COMPLETION. DATED MARCH 31, 2000
THE INFORMATION IN THIS PRELIMINARY PROSPECTUS IS NOT COMPLETE AND MAY BE
CHANGED. THESE SECURITIES MAY NOT BE SOLD UNTIL THE REGISTRATION STATEMENT FILED
WITH THE SECURITIES AND EXCHANGE COMMISSION IS EFFECTIVE. THIS PRELIMINARY
PROSPECTUS IS NOT AN OFFER TO SELL NOR DOES IT SEEK AN OFFER TO BUY THESE
SECURITIES IN ANY JURISDICTION WHERE THE OFFER OR SALE IS NOT PERMITTED.
<PAGE>
                                 81,800 SHARES

                        MILLENNIUM PHARMACEUTICALS, INC.
                                  COMMON STOCK

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

    This prospectus relates to resales of shares of common stock previously
issued by Millennium Pharmaceuticals, Inc. to Abgenix, Inc. The selling
stockholder is offering 81,800 shares of our common stock.

    We will not receive any proceeds from the sale of the shares.

    Abgenix, Inc., or its pledgees, donees, transferees or other
successors-in-interest, may offer the shares from time to time through public or
private transactions at prevailing market prices, at prices related to
prevailing market prices or at privately negotiated prices.

    Our common stock is traded on the Nasdaq National Market under the symbol
"MLNM." On March 30, 2000, the closing price of our common stock on Nasdaq was
$120.375 per share.

    INVESTING IN OUR COMMON STOCK INVOLVES A HIGH DEGREE OF RISK. SEE "RISK
FACTORS" BEGINNING ON PAGE 4.

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

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

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

                      Prospectus dated             , 2000.
<PAGE>
                               TABLE OF CONTENTS

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<CAPTION>
                                                                PAGE
                                                              --------
<S>                                                           <C>
Summary.....................................................      1
The Offering................................................      3
Risk Factors................................................      4
Special Note Regarding Forward-Looking Information..........     12
Use of Proceeds.............................................     13
Selling Stockholder.........................................     13
Description of Capital Stock................................     14
Plan Of Distribution........................................     17
Experts.....................................................     19
Validity Of Common Stock....................................     19
Where You Can Find More Information.........................     19
Incorporation Of Certain Documents By Reference.............     19
</TABLE>

    The Millennium Pharmaceuticals name and logo and the names of products and
services offered by Millennium Pharmaceuticals are trademarks, registered
trademarks, service marks or registered service marks of Millennium
Pharmaceuticals. This prospectus also includes product names, trade names and
trademarks of other companies.

    We have not authorized anyone to provide you with information different from
that contained or incorporated by reference in this prospectus. The selling
stockholder is offering to sell, and seeking offers to buy, shares of our common
stock only in jurisdictions where offers and sales are permitted. The
information contained in this prospectus is accurate only as of the date of this
prospectus, regardless of the time of delivery of this prospectus or of any sale
of common stock.

                                       i
<PAGE>
                                    SUMMARY

    THIS SUMMARY CONTAINS BASIC INFORMATION ABOUT US AND THIS OFFERING. BECAUSE
IT IS A SUMMARY, IT DOES NOT CONTAIN ALL OF THE INFORMATION THAT YOU SHOULD
CONSIDER BEFORE INVESTING. YOU SHOULD READ THE ENTIRE PROSPECTUS CAREFULLY,
INCLUDING THE SECTION ENTITLED "RISK FACTORS" AND OUR CONSOLIDATED FINANCIAL
STATEMENTS AND THE RELATED NOTES BEFORE MAKING AN INVESTMENT DECISION.

                        MILLENNIUM PHARMACEUTICALS, INC.

OUR BUSINESS

    Our goal is to become the biopharmaceutical company of the future by
building on our broad scientific and technological capabilities and methods,
which we call our "technology platform," to develop breakthrough drugs and
predictive medicine products and services. Predictive medicine involves
identifying information that enables healthcare professionals to make better
informed decisions about drug treatment and other aspects of patient care.

    We use many of the same elements of our technology platform throughout our
business, from the discovery of disease-related genes, to the development of
drugs to specifically address these diseases, to the management of patients
affected by these diseases. As a result, we speak of our technological approach
as being applicable from "gene to patient." We continually seek to expand our
technology platform in an effort to increase the speed of drug discovery and
development and improve the resulting drugs.

    We have entered into research, development and commercialization
arrangements, which we call "strategic alliances," with major pharmaceutical and
biotechnology companies relating to a broad range of therapeutic and predictive
medicine products and services. These alliances provide us with the opportunity
to receive royalties and profit sharing, if we and our alliance partners are
successful in developing and commercializing products. In addition, these
alliances provide substantial funding for our research and development and the
continued enhancement of our technology platform.

    We were incorporated in Delaware in 1993. In 1997, we acquired ChemGenics
Pharmaceuticals, Inc. In December 1999, we merged with LeukoSite, Inc. Our
principal executive offices are located at 75 Sidney Street, Cambridge, MA
02139. Our telephone number is (617) 679-7000, and our Internet address is
www.mlnm.com. We do not intend for this reference to our Web site to constitute
incorporation by reference of the information contained at our site. Unless the
context otherwise requires references in this prospectus to "Millennium
Pharmaceuticals," "we," "us," and "our" refer to Millennium
Pharmaceuticals, Inc. and its subsidiaries.

OUR TECHNOLOGY PLATFORM

    Our comprehensive technology platform integrates many of the technologies
used in each step of the therapeutic and diagnostic product discovery and
development processes. Our goal is to increase the efficiency and productivity
of these processes. We seek to use the most advanced technologies available,
whether developed internally by us or licensed by us from third parties.

OUR TARGET MARKETS

    We have three fields of major emphasis:

    - cancer;

    - metabolic diseases, including obesity; and

    - inflammation.

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<PAGE>
    In addition, we have significant programs in infectious diseases,
cardiovascular diseases and diseases of the central nervous system, and we are
engaged in alliances involving the transfer of aspects of our technology.

OUR PRODUCT CANDIDATES

    We expect two of our product candidates to be introduced to the market in
2000: our CAMPATH-Registered Trademark- monoclonal antibody product candidate
and our Melastatin-TM- diagnostic test. We are developing our
CAMPATH-Registered Trademark-monoclonal antibody product candidate through our
partnership with ILEX Oncology. That partnership filed a biologics license
application with the U.S. Food and Drug Administration in December 1999 for the
treatment of patients with chronic lymphocytic leukemia. We are also developing
our Melastatin-TM-diagnostic test for a form of cancer. We are developing this
test with Becton Dickinson through our subsidiary, Millennium Predictive
Medicine, Inc. We have five additional products in clinical trials.

OUR STRATEGIC ALLIANCES

    We have established strategic alliances which are focused on particular
diseases, drug discovery for specific molecular targets, the development of a
specific product candidate or the transfer of elements of our technology
platform. These relationships include alliances with the following companies in
the areas indicated:

    - Taisho Pharmaceuticals--asthma

    - Bristol-Myers Squibb--cancer pharmacogenomics

    - Becton Dickinson--cancer diagnostics

    - Warner-Lambert--inflammation

    - Bayer--cardiovascular diseases, cancer, pain, osteoporosis, liver
      diseases, blood diseases and viral infections

    - Kyowa Hakko--inflammation

    - Monsanto--agriculture and technology transfer

    - Genentech--inflammation

    - American Home Products--central nervous system diseases and bacterial
      infections

    - ILEX Oncology--cancer

    - Eli Lilly--cardiovascular diseases, cancer and protein therapeutics

    - Pfizer--fungal infections

RECENT DEVELOPMENTS

    On January 31, 2000, our board of directors voted to recommend to our
stockholders that our corporate charter be amended to increase the authorized
number of shares of common stock from 100,000,000 shares to 500,000,000 shares.
In addition, on January 31, 2000, our Board of Directors adopted, subject to
stockholder approval, our 2000 Stock Incentive Plan. The 2000 Stock Incentive
Plan would permit the issuance of stock-based awards for a number of shares
equal to 5% of the number of shares of our common stock outstanding on
April 12, 2000, plus an annual increase equal to the lesser of 5% of the number
of shares of our common stock outstanding on the last business day preceding
January 1 in each of 2001, 2002, and 2003 or a lesser amount determined by our
board of directors. These proposals will be considered at our annual meeting of
stockholders to be held on April 12, 2000.

                                       2
<PAGE>
    On February 28, 2000, our board of directors approved a two-for-one split of
our common stock in the form of a stock dividend. Stockholders of record on
March 28, 2000 will be entitled to one additional share of common stock for each
share held on that date. The dividend distribution date will be April 18, 2000.
The stock split is subject to prior approval by our stockholders of an increase
in our authorized common stock at our 2000 annual meeting of stockholders.

    On March 1, 2000, we entered into a merger agreement to acquire the
outstanding shares of Millennium Predictive Medicine that we do not already own,
making it a wholly-owned subsidiary. The transaction will be a stock-for-stock
exchange based on a fixed ratio. This move is intended to more closely align our
therapeutic and predictive medicine discovery and development efforts. Under the
terms of the agreement, Millennium Predictive Medicine stockholders will receive
a total of 560,186 shares of our common stock, subject to adjustment for the
two-for-one stock split described above.

    On March 6, 2000, we entered into a collaboration agreement with
Abgenix, Inc. which provides us with access to Abgenix's XenoMouse-TM-technology
for the creation of fully human antibodies. Under this agreement, we will have
broad access to the XenoMouse-TM- technology for research purposes as well as
commercial use. We have agreed to make an upfront payment and future payments
that could reach $100 million plus royalties on product sales for which we will
receive a specified number of commercial licenses. A portion of the upfront
payment consisted of shares of our common stock and all or portions of future
payments may also consist of shares of our common stock. Under the terms of the
collaboration agreement, we are obligated to register the shares of our common
stock issued to Abgenix as part of the upfront payment and any future payments.
With this registration statement and prospectus, we are fulfilling our
obligation to register the shares of our common stock issued to Abgenix as part
of the upfront payment.

                                  THE OFFERING

<TABLE>
<S>                                    <C>
Common Stock offered by the
selling..............................  81,800 shares stockholder

Use of Proceeds......................  Millennium Pharmaceuticals will not receive any proceeds
                                       from the sale of shares in this offering.

Nasdaq symbol........................  Our common stock is traded on the Nasdaq National Market
                                       under the symbol: MLNM.
</TABLE>

                                       3
<PAGE>
                                  RISK FACTORS

    AN INVESTMENT IN THE SECURITIES OFFERED HEREBY INVOLVES A HIGH DEGREE OF
RISK. IN ADDITION TO THE OTHER INFORMATION SET FORTH OR INCORPORATED BY
REFERENCE IN THIS PROSPECTUS, THE FOLLOWING RISK FACTORS SHOULD BE CONSIDERED
CAREFULLY IN EVALUATING US AND OUR BUSINESS BEFORE INVESTING IN THE SECURITIES
OFFERED BY THIS PROSPECTUS. IF ANY OF THE FOLLOWING EVENTS ACTUALLY OCCURS, OUR
BUSINESS, FINANCIAL CONDITION AND RESULTS OF OPERATIONS WOULD LIKELY SUFFER,
POSSIBLY MATERIALLY.

REGULATORY RISKS

IF CLINICAL TRIALS OF OUR PRODUCT CANDIDATES ARE NOT SUCCESSFUL, WE WILL NOT BE
ABLE TO COMPLETE DEVELOPMENT OF OR SELL THESE PRODUCT CANDIDATES

    In order to obtain regulatory approvals for the commercial sale of any
products, we or our alliance partners must demonstrate through preclinical
testing and clinical trials that the product is safe and effective. Before our
merger with LeukoSite, Inc. in December 1999, neither we nor any of our alliance
partners had initiated human clinical trials with respect to any product or
service based upon our discoveries or filed an investigational new drug
application with the United States Food and Drug Administration, or FDA, to do
so.

IF WE DO NOT OBTAIN REGULATORY APPROVALS, WE WILL NOT BE ABLE TO INITIATE
CLINICAL TRIALS OR MARKET ANY PRODUCTS

    We must obtain regulatory approvals for our ongoing development activities
and before marketing or selling any products. We may not receive regulatory
approvals to conduct clinical trials of our products or to manufacture or market
our products. In particular, we may not receive regulatory approval from the FDA
or any other regulatory authority to market CAMPATH-Registered Trademark-
monoclonal antibody, our most advanced product candidate.

WE EXPECT TO INCUR SIGNIFICANT COSTS AND TIME DELAYS IN THE REGULATORY PROCESS,
WHICH WILL MATERIALLY AFFECT OUR REVENUES AND CASH REQUIREMENTS

    The process of obtaining FDA and other required regulatory approvals,
including approvals in other countries, is lengthy and expensive. The time
required for FDA and other clearances or approvals is uncertain and typically
takes a number of years. Any delay in obtaining or failure to obtain required
clearance or approvals could materially adversely affect our ability to generate
revenues from the affected product or service. We have only limited experience
in filing and prosecuting applications necessary to gain regulatory approvals.

    Certain of the products that are likely to result from our research and
development programs may be based on new technologies and new therapeutic
approaches that have not been extensively tested in humans. The regulatory
requirements governing these types of products may be more rigorous than for
conventional products. As a result, we may experience a longer regulatory
process in connection with any products that we develop based on these new
technologies or new therapeutic approaches.

    We also are subject to numerous and varying foreign regulatory requirements
governing the design and conduct of clinical trials and the manufacturing and
marketing of our future products and some types of services. The approval
procedure varies among countries. Foreign approvals may take longer than FDA
approval. Approval by the FDA does not ensure approval by regulatory authorities
in other countries.

    All of these regulatory risks also are applicable to development,
manufacturing and marketing undertaken by our alliance partners or other
collaborators.

                                       4
<PAGE>
RISKS RELATING TO OUR INDUSTRY, BUSINESS AND STRATEGY

BECAUSE THE GENOMICS INDUSTRY IS NEW, IT IS POSSIBLE THAT THE DISCOVERIES AND
TECHNOLOGY ON WHICH THIS INDUSTRY IS BASED WILL NOT RESULT IN COMMERCIAL
PRODUCTS OR SERVICES

    The genomics industry is new and evolving rapidly. We focus our genomics
research primarily on diseases that may be linked to several or many genes
working in combination. Both we and the general scientific and medical
communities have only a limited understanding relating to the role of genes and
their products in these diseases. To date, we have not commercialized any
products or services, and we may not be successful in doing so in the future. In
addition, relatively few products based on gene discoveries have been developed
and commercialized by others. Rapid technological development by us or others
may result in compounds, products or processes becoming obsolete before we
recover our development expenses.

WE HAVE NOT YET RECEIVED MARKETING APPROVAL FOR ANY PRODUCT OR SERVICE RESULTING
FROM OUR DEVELOPMENT EFFORTS AND MAY NOT BE ABLE TO OBTAIN ANY SUCH APPROVAL

    We have completed development of only one product,
CAMPATH-Registered Trademark- monoclonal antibody, and have only recently
applied to the FDA for approval to market this product. All of the other
products that we are developing will require additional research and
development, extensive preclinical studies and clinical trials and regulatory
approval prior to any commercial sales. We may need to successfully address a
number of technological challenges in order to complete development of any of
our products. Moreover, these products may not be effective in treating any
disease or may prove to have undesirable or unintended side effects, toxicities
or other characteristics that may prevent or limit commercial use.

OUR PLAN TO GROW THROUGH ACQUISITIONS OF OTHER COMPANIES WILL NOT BE SUCCESSFUL
IF WE ARE UNABLE TO INTEGRATE ACQUIRED COMPANIES WITH OUR OTHER OPERATIONS OR IF
THE TECHNOLOGY OR PERSONNEL OF ACQUIRED COMPANIES DO NOT MEET OUR EXPECTATIONS

    We completed our merger with LeukoSite on December 22, 1999. We may not be
able to successfully integrate or profitably manage LeukoSite's businesses. In
addition, the combination of our business with LeukoSite's may not achieve
revenues, net income or loss levels, efficiencies or synergies that justify the
merger. The combined company may experience slower rates of growth as compared
to the historical rates of growth of Millennium and LeukoSite independently. We
plan to make additional acquisitions in the future, which will entail similar
risks.

COMPETITION FOR SCIENTIFIC AND MANAGERIAL PERSONNEL IN OUR INDUSTRY IS INTENSE;
WE WILL NOT BE ABLE TO SUSTAIN OUR OPERATIONS AND GROW IF WE ARE NOT ABLE TO
ATTRACT AND RETAIN KEY PERSONNEL

    Our success substantially depends on the ability, experience and performance
of our senior management and other key personnel. If we lose one or more of the
members of our senior management or other key employees, our business and
operating results could be seriously harmed.

    In addition, our future success will depend heavily on our ability to
continue to hire, train, retain and motivate additional skilled managerial and
scientific personnel. The pool of personnel with the skills that we require is
limited. Competition to hire from this limited pool is intense.

    The stock options held by LeukoSite employees became fully vested upon the
closing of our acquisition of LeukoSite. This acceleration may adversely affect
our ability to retain former LeukoSite employees.

                                       5
<PAGE>
WE FACE SUBSTANTIAL COMPETITION, WHICH MAY RESULT IN OTHERS DISCOVERING,
DEVELOPING OR COMMERCIALIZING PRODUCTS AND SERVICES BEFORE OR MORE SUCCESSFULLY
THAN WE DO

    The fields of genomics, biotechnology and pharmaceuticals are highly
competitive. Many of our competitors are substantially larger than we are and
have substantially greater capital resources, research and development staffs
and facilities than we have. Furthermore, many of our competitors are more
experienced than we are in drug discovery, development and commercialization,
obtaining regulatory approvals and product manufacturing and marketing. As a
result, our competitors may identify genes associated with diseases or discover,
develop and commercialize products or services based on such genes before we do.
In addition, our competitors may discover, develop and commercialize products or
services which render non-competitive or obsolete the products or services that
we or our strategic alliance partners are seeking to develop and commercialize.

WE MAY NOT BE ABLE TO OBTAIN BIOLOGICAL MATERIAL, INCLUDING HUMAN AND ANIMAL DNA
SAMPLES, REQUIRED FOR OUR GENETIC STUDIES, WHICH COULD DELAY OR IMPEDE OUR DRUG
DISCOVERY EFFORTS

    Our gene identification strategy includes genetic studies of families and
populations prone to particular diseases. These studies require the collection
of large numbers of DNA samples from affected individuals, their families and
other suitable populations as well as animal models. The availability of DNA
samples and other biological material is important to our ability to discover
the genes responsible for human diseases through human genetic approaches and
other studies. Competition for these resources is intense. Access to suitable
populations, materials and samples could be limited by forces beyond our
control, including governmental actions. Some of our competitors may have
obtained access to significantly more family and population resources and
biological materials than we have obtained. As a result, we may not be able to
obtain access to DNA samples necessary to support our human gene discovery
programs.

RISKS RELATING TO OUR FINANCIAL RESULTS AND STRUCTURE AND NEED FOR FINANCING

WE HAVE INCURRED SUBSTANTIAL LOSSES, WE EXPECT TO CONTINUE TO INCUR LOSSES AND
WE WILL NOT BE SUCCESSFUL UNLESS WE REVERSE THIS TREND

    We have incurred losses in four of the last six years, including the year
ended December 31, 1999. We expect to continue to incur substantial operating
losses in future periods. To date, substantially all of our revenues have
resulted from payments from strategic alliance partners. We have not received
any revenues from the sale of products or clinical or diagnostic services.

    We expect to increase our spending significantly as we continue to expand
our infrastructure, research and development programs and commercialization
activities. As a result, we will need to generate significant revenues to pay
these costs and achieve profitability. We cannot be certain whether or when we
will become profitable because of the significant uncertainties with respect to
our ability to generate revenues from the sale of products and services and from
existing and potential future strategic alliances.

OUR SUBSTANTIAL INDEBTEDNESS MAY ADVERSELY AFFECT OUR CASH FLOW AND OPERATIONS
AND BE DIFFICULT FOR US TO REPAY, WHICH COULD ADVERSELY AFFECT THE VALUE OF YOUR
INVESTMENT IN US

    We have substantial amounts of outstanding indebtedness, primarily our 5.50%
convertible subordinated notes due January 15, 2007. We also may obtain
additional long term debt and working capital lines of credit. As a result of
this indebtedness, our principal and interest payment obligations are
substantial. There is the possibility that we may be unable to generate cash
sufficient to pay the principal of, interest on and other amounts due in respect
of our indebtedness when due. In particular, we may require funds from external
sources, such as new borrowings, to repay our 5.50% convertible

                                       6
<PAGE>
subordinated notes when their entire principal amounts become due in a single
payment on their maturity date.

    Our substantial leverage could have significant negative consequences,
including:

    - increasing our vulnerability to general adverse economic and industry
      conditions;

    - limiting our ability to obtain additional financing;

    - requiring the dedication of a substantial portion of our cash from
      operations to service our indebtedness, thereby reducing the amount of our
      cash available for other purposes, including capital expenditures;

    - limiting our flexibility in planning for, or reacting to, changes in our
      business and the industry in which we compete; and

    - placing us at a possible competitive disadvantage vis-a-vis less leveraged
      competitors and competitors that have better access to capital resources.

WE MAY NEED ADDITIONAL FINANCING, WHICH MAY BE DIFFICULT TO OBTAIN; OUR FAILURE
TO OBTAIN NECESSARY FINANCING OR DOING SO ON UNATTRACTIVE TERMS COULD AVERSELY
AFFECT OUR DISCOVERY AND DEVELOPMENT PROGRAMS AND OTHER OPERATIONS

    We will require substantial funds to conduct research and development,
including preclinical testing and clinical trials of our potential products,
meet our obligations to our strategic alliance partners, manufacture and market
any products and services that are approved for commercial sale and meet our
debt service obligations. Additional financing may not be available when we need
it or may not be available on terms that are favorable to us.

    If we are unable to obtain adequate funding on a timely basis, we may be
required to significantly curtail one or more of our discovery or development
programs. We could be required to seek funds through arrangements with
collaborative partners or others that may require us to relinquish rights to
certain of our technologies, product candidates or products which we would
otherwise pursue on our own.

RISKS RELATING TO STRATEGIC ALLIANCE PARTNERS

WE DEPEND SIGNIFICANTLY ON OUR STRATEGIC ALLIANCE PARTNERS TO DEVELOP AND
COMMERCIALIZE PRODUCTS AND SERVICES BASED ON OUR WORK; OUR BUSINESS MAY SUFFER
IF ANY OF OUR STRATEGIC ALLIANCE PARTNERS BREACHES THEIR AGREEMENT OR FAILS TO
SUPPORT OR TERMINATES THEIR ALLIANCE WITH US

    We conduct most of our discovery and development activities through
strategic alliances. The success of these programs depends heavily on the
efforts and activities of our strategic alliance partners. Each of our alliance
partners has significant discretion in determining the efforts and resources
that they will apply to the alliance. Our existing and any future alliances may
not be scientifically or commercially successful.

    The risks that we face in connection with these alliances include:

    - All of our strategic alliance agreements are subject to termination under
      various circumstances, including in many cases on short notice without
      cause.

    - In our strategic alliance agreements, we generally agree not to conduct
      specified types of research and development in the field that is the
      subject of the alliance. These agreements may have the effect of limiting
      the areas of research and development we may pursue, either alone or in
      collaboration with third parties.

                                       7
<PAGE>
    - Our alliance partners may develop and commercialize, either alone or with
      others, products and services that are similar to or competitive with the
      products and services that are the subject of the alliance with us.

    - Our alliance partners may change the focus of their development and
      commercialization efforts. Pharmaceutical and biotechnology companies
      historically have re-evaluated their priorities following mergers and
      consolidations, which have been common in recent years in these
      industries.

    - We will rely on our alliance partners to manufacture most products covered
      by our alliances. For example, Becton Dickinson has the sole right to
      manufacture Melastatin-TM-.

WE MAY NOT BE SUCCESSFUL IN ESTABLISHING ADDITIONAL STRATEGIC ALLIANCES, WHICH
COULD ADVERSELY AFFECT OUR ABILITY TO DEVELOP AND COMMERCIALIZE PRODUCTS

    An important element of our business strategy is entering into strategic
alliances for the development and commercialization of products and services
based on our discoveries. We face significant competition in seeking appropriate
alliance partners. Moreover, these alliance arrangements are complex to
negotiate and time-consuming to document. We may not be successful in our
efforts to establish additional strategic alliances or other alternative
arrangements. The terms of any additional strategic alliances or other
arrangements that we establish may not be favorable to us. Moreover, such
strategic alliances or other arrangements may not be successful.

RISKS RELATING TO INTELLECTUAL PROPERTY

IF WE ARE UNABLE TO OBTAIN PATENT PROTECTION FOR OUR DISCOVERIES, THE VALUE OF
OUR TECHNOLOGY AND PRODUCTS WILL BE ADVERSELY AFFECTED; IF WE INFRINGE PATENT OR
OTHER INTELLECTUAL PROPERTY RIGHTS OF THIRD PARTIES, WE MAY NOT BE ABLE TO
DEVELOP AND COMMERCIALIZE OUR PRODUCTS AND SERVICES OR THE COST OF DOING SO MAY
INCREASE

    Our patent positions, and those of other pharmaceutical and biotechnology
companies, are generally uncertain and involve complex legal, scientific and
factual questions.

    Our ability to develop and commercialize products and services depends in
significant part on our ability to:

    - Obtain patents;

    - Obtain licenses to the proprietary rights of others on commercially
      reasonable terms;

    - Operate without infringing upon the proprietary rights of others;

    - Prevent others from infringing on our proprietary rights; and

    - Protect trade secrets.

THERE IS SIGNIFICANT UNCERTAINTY ABOUT THE VALIDITY AND PERMISSIBLE SCOPE OF
GENOMICS PATENTS IN OUR INDUSTRY, WHICH MAY MAKE IT DIFFICULT FOR US TO OBTAIN
PATENT PROTECTION FOR OUR DISCOVERIES

    The validity and permissible scope of patent claims in the pharmaceutical
and biotechnology fields, including the genomics field, involve important
unresolved legal principles. For example, there is significant uncertainty both
in the United States and abroad regarding the patentability of gene sequences in
the absence of functional data and the scope of patent protection available for
full-length genes and partial gene sequences. Moreover, certain groups have made
certain gene sequences available in publicly accessible databases. These and
other disclosures may adversely affect our ability to obtain patent protection
for gene sequences claimed by us in patent applications that we file subsequent
to such disclosures. There is also some uncertainty as to whether human clinical
data will

                                       8
<PAGE>
be required for issuance of patents for human therapeutics. If such data are
required, our ability to obtain patent protection could be delayed or otherwise
adversely affected.

THIRD PARTIES MAY OWN OR CONTROL PATENTS OR PATENT APPLICATIONS AND REQUIRE US
TO SEEK LICENSES, WHICH COULD INCREASE OUR DEVELOPMENT AND COMMERCIALIZATION
COSTS, OR PREVENT US FROM DEVELOPING OR MARKETING PRODUCT OR SERVICE CANDIDATES

    We may not have rights under some patents or patent applications related to
our proposed products, processes or services. Third parties may own or control
these patents and patent applications in the United States and abroad.
Therefore, in some cases, such as those described below, to develop,
manufacture, sell or import certain of our proposed products, processes or
services, we or our alliance partners may choose to seek, or be required to
seek, licenses under third party patents issued in the United States and abroad
or those which might issue from United States and foreign patent applications.
If licenses are not available to us on acceptable terms, we or our alliance
partners may not be able to develop, manufacture, sell or import these products,
processes or services.

    With respect to our product candidate LDP-01, we are aware of third party
patents and patent applications which relate to certain anti-CD18 antibodies and
their use in various methods of treatment including methods of reperfusion
therapy and methods of treating focal ischemic stroke. In addition, our LDP-01,
LDP-02, and CAMPATH-Registered Trademark- product candidates are humanized
monoclonal antibodies. We are aware of third party patents and patent
applications which relate to certain humanized or modified antibodies, products
useful for making humanized or modified antibodies, and processes for making and
using humanized or modified antibodies. We are also aware of third party patents
and patent applications relating to certain manufacturing processes, products
thereof and materials useful in such processes.

    Our product candidates LDP-977, LDP-341, and LDP-519 are all small molecule
drug candidates. With respect to LDP-341, we are aware of third party patents or
patent applications which relate to either intermediates or synthetic processes
used in the synthesis of these compounds. Additionally, for the use of LDP-341
and LDP-519 in the treatment of infarctions we are aware of the existence of a
potentially interfering patent application filed by one of our former
consultants.

WE MAY BECOME INVOLVED IN EXPENSIVE PATENT LITIGATION OR OTHER PROCEEDINGS,
WHICH COULD RESULT IN OUR INCURRING SUBSTANTIAL COSTS AND EXPENSES OR
SUBSTANTIAL LIABILITY FOR DAMAGES OR REQUIRE US TO STOP OUR DEVELOPMENT AND
COMMERCIALIZATION EFFORTS

    There has been substantial litigation and other proceedings regarding the
patent and other intellectual property rights in the pharmaceutical and
biotechnology industries. We may become a party to patent litigation or other
proceedings regarding intellectual property rights. For example, we believe that
we hold patent applications that cover genes that are also claimed in patent
applications filed by others. Interference proceedings before the United States
Patent and Trademark Office may be necessary to establish which party was the
first to invent these genes.

    The cost to us of any patent litigation or other proceeding, even if
resolved in our favor, could be substantial. Some of our competitors may be able
to sustain the cost of such litigation or proceedings more effectively than we
can because of their substantially greater financial resources. If a patent
litigation or other proceeding is resolved against us, we or our alliance
partners may be enjoined from developing, manufacturing, selling or importing
our products, processes or services without a license from the other party and
we may be held liable for significant damages. We may not be able to obtain any
required license on commercially acceptable terms or at all.

    Uncertainties resulting from the initiation and continuation of patent
litigation or other proceedings could have a material adverse effect on our
ability to compete in the marketplace. Patent litigation and other proceedings
may also absorb significant management time.

                                       9
<PAGE>
RISKS RELATING TO PRODUCT MANUFACTURING, MARKETING AND SALES

BECAUSE MANY OF THE PRODUCTS AND SERVICES THAT WE DEVELOP WILL BE BASED ON NEW
TECHNOLOGIES AND THERAPEUTIC APPROACHES, THE MARKET MAY NOT BE RECEPTIVE TO
THESE PRODUCTS AND SERVICES UPON THEIR INTRODUCTION

    The commercial success of our products and services that are approved for
marketing will depend upon their acceptance by the medical community and third
party payors as clinically useful, cost effective and safe. Many of the products
and services that we are developing are based upon new technologies or
therapeutic approaches. As a result, it may be more difficult for us to achieve
market acceptance of our products and services, particularly the first products
and services that we introduce to the market based on new technologies and
therapeutic approaches.

BECAUSE WE HAVE NO SALES, MARKETING OR DISTRIBUTION EXPERIENCE AND CAPABILITIES,
WE WILL BE DEPENDENT ON THIRD PARTIES TO SUCCESSFULLY PERFORM THESE FUNCTIONS OR
WILL BE REQUIRED TO INCUR SIGNIFICANT COSTS AND DEVOTE SIGNIFICANT EFFORTS TO
DEVELOP THESE CAPABILITIES

    We have no sales, marketing or distribution experience and capabilities. We
plan to rely significantly on sales, marketing and distribution arrangements
with our strategic alliance partners and other third parties for the products
and services that we are developing. For example, our partnership that holds
CAMPATH-Registered Trademark- monoclonal antibody will rely solely upon Schering
AG and its U.S. affiliate, Berlex Laboratories, for the marketing, distribution
and sale of the CAMPATH-Registered Trademark- product throughout the world other
than the Far East. If in the future we determine to perform sales, marketing and
distribution functions ourselves, we would face a number of additional risks,
including the need to recruit experienced marketing and sales personnel.

BECAUSE WE HAVE LIMITED MANUFACTURING CAPABILITIES, WE WILL BE DEPENDENT ON
THIRD PARTY MANUFACTURERS TO MANUFACTURE PRODUCTS FOR US OR WILL BE REQUIRED TO
INCUR SIGNIFICANT COSTS AND DEVOTE SIGNIFICANT EFFORTS TO ESTABLISH OUR OWN
MANUFACTURING FACILITIES AND CAPABILITIES

    We have limited manufacturing experience and no commercial scale
manufacturing capabilities. In order to continue to develop products and
services, apply for regulatory approvals and, ultimately, commercialize any
products and services, we will need to develop, contract for or otherwise
arrange for the necessary manufacturing capabilities.

    We currently rely upon third parties to produce material for preclinical
testing purposes and expect to continue to do so in the future. We also expect
to rely upon other third parties, including our strategic alliance partners, to
produce materials required for clinical trials and for the commercial production
of certain of our products if we succeed in obtaining necessary regulatory
approvals. Our partnership with ILEX Oncology relies on Boehringer Ingleheim as
the sole source manufacturer of CAMPATH-Registered Trademark- monoclonal
antibody. There are a limited number of manufacturers that operate under the
FDA's good manufacturing practices regulations capable of manufacturing for us.
If we are unable to arrange for third party manufacturing of our products, or to
do so on commercially reasonable terms, we may not be able to complete
development of our products or market them.

    We may in the future determine to manufacture certain of our products in our
own manufacturing facilities. We will require substantial additional funds and
need to recruit qualified personnel in order to build or lease and operate any
manufacturing facilities.

IF WE FAIL TO OBTAIN AN ADEQUATE LEVEL OF REIMBURSEMENT FOR OUR FUTURE PRODUCTS
OR SERVICES BY THIRD PARTY PAYORS, THERE MAY BE NO COMMERCIALLY VIABLE MARKETS
FOR OUR PRODUCTS OR SERVICES

    The availability and levels of reimbursement by governmental and other third
party payors affects the market for any pharmaceutical product or healthcare
service. These third party payors continually

                                       10
<PAGE>
attempt to contain or reduce the costs of healthcare by challenging the prices
charged for medical products and services. In certain foreign countries,
particularly the countries of the European Union, the pricing of prescription
pharmaceuticals is subject to governmental control. We may not be able to sell
our products and services profitably if reimbursement is unavailable or limited
in scope or amount.

    In both the United States and certain foreign jurisdictions, there have been
a number of legislative and regulatory proposals to change the healthcare
system. Further proposals are likely. The potential for adoption of these
proposals affects or will affect our ability to raise capital, obtain additional
collaborative partners and market our products.

    If we or our alliance partners obtain marketing approvals for our products
and services, we expect to experience pricing pressure due to the trend toward
managed health care, the increasing influence of health maintenance
organizations and additional legislative proposals.

ETHICAL, LEGAL AND SOCIAL ISSUES RELATED TO GENETIC TESTING MAY CAUSE OUR
DIAGNOSTIC PRODUCTS TO BE REJECTED BY CUSTOMERS OR PROHIBITED OR CURTAILED BY
GOVERNMENTAL AUTHORITIES

    Diagnostic tests that evaluate genetic predisposition to disease raise
issues regarding the use and confidentiality of the information provided by such
tests. Insurance carriers and employers might discriminate on the basis of such
information, resulting in a significant barrier to the acceptance of such tests
by customers. This type of discrimination could cause governmental authorities
to prohibit or limit the use of such tests.

RISKS RELATING TO AN INVESTMENT IN OUR COMMON STOCK

WE HAVE ANTI-TAKEOVER DEFENSES THAT COULD DELAY OR PREVENT A TAKEOVER THAT
STOCKHOLDERS MAY CONSIDER FAVORABLE

    Certain provisions of our certificate of incorporation and bylaws and of
Delaware law could have the effect of delaying, deferring or preventing an
acquisition of Millennium Pharmaceuticals. For example, we have divided our
board of directors into three classes that serve staggered three-year terms, we
may authorize the issuance of up to 5,000,000 shares of "blank check" preferred
stock, our stockholders may not take actions by written consent and our
stockholders are limited in their ability to introduce proposals at stockholder
meetings.

OUR STOCK PRICE COULD BE VOLATILE, WHICH COULD CAUSE YOU TO LOSE PART OR ALL OF
YOUR INVESTMENT

    The market price of our common stock, like that of the common stock of many
other biotechnology companies, may be highly volatile. Factors such as:

    - announcements of technological innovations or new commercial products by
      us or our competitors,

    - disclosure of results of clinical testing or regulatory proceedings,

    - governmental regulation and approvals,

    - developments in patent or other proprietary rights including as a result
      of any public policy concerns,

    - public concern as to the safety of products developed by us,

    - our financial results, and

    - general market conditions

may have a significant effect on the market price of our common stock. In
addition, the stock market has experienced extreme price and volume
fluctuations. This volatility has significantly affected the market prices of
securities of many biotechnology and pharmaceutical companies for reasons
frequently unrelated to or disproportionate to the operating performance of the
specific companies. These broad market fluctuations may adversely affect the
market price of our common stock.

                                       11
<PAGE>
               SPECIAL NOTE REGARDING FORWARD-LOOKING INFORMATION

    This prospectus and the documents incorporated by reference in this
prospectus contain "forward-looking statements" within the meaning of
Section 27A of the Securities Act of 1933, and Section 21E of the Securities
Exchange Act of 1934 that involve risks and uncertainties, such as statements
concerning:

- - growth and future operating results

- - developments in our markets and strategic focus;

- - potential acquisitions and the integration of acquired businesses, products
  and technologies;

- - intellectual property;

- - discovery and development of products;

- - new products;

- - strategic alliances;

- - our manufacturing, marketing, sales and distribution capabilities; and

- - future economic business and regulatory conditions

    Words such as "project," "believe," "anticipate," "plan," "expect,"
"estimate," "intend," "should," "would," "could" or "may," or other words that
convey uncertainty of future events or outcome generally accompany these
forward-looking statements. This prospectus discloses important factors that
could cause actual results to differ materially from these expectations,
including the "Risk Factors" beginning on page 4. You should read these factors
and other cautionary statements made in this prospectus and the documents
incorporated by reference as being applicable to all related forward-looking
statements whenever they appear in this prospectus and the documents
incorporated by reference. We assume no obligation to update them even though
our situation may change in the future.

                                       12
<PAGE>
                                USE OF PROCEEDS

    We will not receive any proceeds from the sale of shares by the selling
stockholder.

    The selling stockholder will pay any underwriting discounts and commissions
and expenses incurred by the selling stockholder for brokerage, accounting, tax
or legal services or any other expenses incurred by the selling stockholder in
disposing of the shares. We will bear all other costs, fees and expenses
incurred in effecting the registration of the shares covered by this prospectus,
including, without limitation, all registration and filing fees, Nasdaq listing
fees and fees and expenses of our counsel and our accountants.

                              SELLING STOCKHOLDER

    We issued the shares of common stock covered by this prospectus in a private
placement in connection with our collaboration agreement with Abgenix, Inc. The
following table sets forth, to our knowledge, certain information about the
selling stockholder as of March 27, 2000.

    Beneficial ownership is determined in accordance with the rules of the
Securities and Exchange Commission, and includes voting or investment power with
respect to shares. Unless otherwise indicated below, to our knowledge, the
selling stockholder named in the table has sole voting and investment power with
respect to its shares of common stock. The inclusion of any shares in this table
does not constitute an admission of beneficial ownership for the person named
below.

<TABLE>
<CAPTION>
                                              SHARES OF COMMON                        SHARES OF COMMON
                                             STOCK BENEFICIALLY                          STOCK TO BE
                                               OWNED PRIOR TO         NUMBER OF      BENEFICIALLY OWNED
                                                  OFFERING            SHARES OF      AFTER OFFERING (1)
             NAME OF SELLING                ---------------------   COMMON STOCK    ---------------------
               STOCKHOLDER                   NUMBER    PERCENTAGE   BEING OFFERED    NUMBER    PERCENTAGE
- ------------------------------------------   ------    ----------   -------------    ------    ----------
<S>                                         <C>        <C>          <C>             <C>        <C>
Abgenix, Inc..............................   81,800            *       81,800           0           0%
</TABLE>

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

*   Less than one percent.

1.  We do not know when or in what amounts a selling stockholder may offer
    shares for sale. Because the selling stockholder may offer all or some of
    the shares pursuant to this offering, and because there are currently no
    agreements, arrangements or understandings with respect to the sale of any
    of the shares, we can not estimate the number of the shares that will be
    held by the selling stockholder after completion of the offering. However,
    for purposes of this table, we have assumed that, after completion of the
    offering, none of the shares covered by this prospectus will be held by the
    selling stockholder.

                                       13
<PAGE>
                          DESCRIPTION OF CAPITAL STOCK

    We are authorized by our charter to issue 100,000,000 shares of common
stock, $0.001 par value per share, of which 45,392,092 shares were issued and
outstanding on February 29, 2000, and 5,000,000 shares of undesignated preferred
stock, $.001 par value per share, of which no shares are issued and outstanding.
On February 28, 2000, we announced a two-for-one stock split of our common
stock, to be effected in the form of a stock dividend to be distributed on
April 18, 2000 to stockholders of record on March 28, 2000. This dividend is
conditioned on the approval by our stockholders at the 2000 annual meeting of
Stockholders of an amendment to our charter increasing the number of shares of
common stock authorized for issuance to 500,000,000 shares. The annual meeting
of stockholders will be held on April 12, 2000.

COMMON STOCK

    VOTING.  Holders of common stock are entitled to one vote for each share
held on all matters submitted to a vote of stockholders and do not have
cumulative voting rights. Accordingly, holders of a majority of the shares of
common stock entitled to vote in any election of directors may elect all of the
directors standing for election.

    DIVIDENDS.  If our board of directors declares a dividend, holders of common
stock will receive payments on a ratable basis from our funds that are legally
available to pay dividends. However, this dividend right is subject to any
preferential dividend rights we may grant to the persons who hold preferred
stock, if any is outstanding.

    LIQUIDATION.  If we are dissolved, the holders of our common stock will be
entitled to share ratably in all the assets that remain after we pay our
liabilities and any amounts we may owe to the persons who hold preferred stock,
if any is outstanding.

    OTHER.  Holders of our common stock do not have preemptive, subscription,
redemption or conversion rights. The outstanding shares of our common stock are
fully paid and nonassessable.

PREFERRED STOCK

    Our board of directors is authorized, subject to any limitations prescribed
by law, without further stockholder approval, to issue from time to time up to
5,000,000 shares of preferred stock, in one or more series. Each such series of
preferred stock shall have such number of shares, designations, preferences,
voting powers, qualifications and special or relative rights or privileges as
shall be determined by our board of directors, which may include, among others,
dividend rights, voting rights, redemption and sinking fund provisions,
liquidation preferences, conversion rights and preemptive rights.

    Our stockholders have granted the board of directors authority to issue the
preferred stock and to determine its rights and preferences in order to
eliminate delays associated with a stockholder vote on specific issuances. The
rights of the holders of common stock will be subject to, and may be adversely
affected by, the rights of holders of any preferred stock that may be issued in
the future. The issuance of preferred stock, while providing desirable
flexibility in connection with possible acquisitions and other corporate
purposes, could have the effect of making it more difficult for a third party to
acquire, or of discouraging a third party from attempting to acquire, a majority
of our outstanding voting stock. We have no present plans to issue any shares of
preferred stock.

                                       14
<PAGE>
WARRANTS

    As of February 29, 2000, there were outstanding warrants to purchase an
aggregate of 316,885 shares of common stock, at exercise prices ranging from
$3.00 per share to $37.76 per share. None of the warrants confer upon their
holders any rights as stockholders.

DELAWARE LAW AND CERTAIN CHARTER AND BY-LAW PROVISIONS

    BUSINESS COMBINATIONS.  We are subject to the provisions of Section 203 of
the General Corporation Law of Delaware. Section 203 prohibits a publicly-held
Delaware corporation from engaging in a "business combination" with an
"interested stockholder" for a period of three years after the date of the
transaction in which the person became an interested stockholder, unless the
business combination is approved in a prescribed manner. A "business
combination" includes mergers, asset sales and other transactions resulting in a
financial benefit to the interested stockholder. Subject to certain exceptions,
an "interested stockholder" is a person who, together with affiliates and
associates, owns, or within three years did own, 15% or more of the
corporation's voting stock.

    STAGGERED BOARD.  Our charter provides for the division of the board of
directors into three classes as nearly equal in size as possible with staggered
three-year terms. In addition, our certificate of incorporation provides that
directors may be removed only for cause by the affirmative vote of the holders
of two-thirds of the shares of capital stock of the corporation entitled to
vote. Under our certificate of incorporation, any vacancy on the board of
directors, however occurring, including a vacancy resulting from an enlargement
of the board, may only be filled by vote of a majority of the directors then in
office. The classification of the board of directors and the limitations on the
removal of directors and filling of vacancies could have the effect of making it
more difficult for a third party to acquire, or of discouraging a third party
from acquiring, control of Millennium Pharmaceuticals.

    SUPERMAJORITY VOTES REQUIRED.  The Corporation Law of Delaware provides
generally that the affirmative vote of a majority of the shares entitled to vote
on any matter is required to amend a corporation's certificate of incorporation
or bylaws, unless a corporation's certificate of incorporation or bylaws, as the
case may be, requires a greater percentage. Our certificate of incorporation and
the bylaws require the affirmative vote of the holders of at least 75% of the
shares of our common stock issued and outstanding and entitled to vote to amend
or repeal any of the provisions described in the prior paragraph.

    INDEMNIFICATION.  Our charter contains provisions permitted under the
Corporation Law of Delaware relating to the liability of directors. The
provisions eliminate a director's liability for monetary damages for a breach of
fiduciary duty, except in circumstances involving wrongful acts, such as the
breach of a director's duty of loyalty or acts or omissions which involve
intentional misconduct or a knowing violation of law. The limitation of
liability described above does not alter the liability of our directors and
officers under federal securities laws. Furthermore, our certificate of
incorporation contains provisions to indemnify our directors and officers to the
fullest extent permitted by the Corporation Law of Delaware. These provisions do
not limit or eliminate the right of Millennium Pharmaceuticals or any
shareholder to seek non-monetary relief such as an injunction or rescission in
the event of a breach by a director or an officer of his duty of care to
Millennium Pharmaceuticals. We believe that these provisions will assist us in
attracting and retaining qualified individuals to serve as directors.

    STOCKHOLDER ACTION; SPECIAL MEETING OF STOCKHOLDERS.  Our certificate of
incorporation provides that stockholders may take action only at a duly called
annual or special meeting of stockholders and may not take action by written
consent. Our certificate of incorporation further provides that special meetings
of our stockholders may be called only by the chairman of the board of
directors, by a

                                       15
<PAGE>
majority of the board of directors or by our Chief Executive Officer, and in no
event may the stockholders call a special meeting.

    ADVANCE NOTICE REQUIREMENTS FOR STOCKHOLDER PROPOSALS AND DIRECTOR
NOMINATIONS.  Our bylaws provide that stockholders seeking to bring business
before an annual meeting of stockholders, or to nominate candidates for election
as directors at an annual meeting of stockholders, must meet certain procedural
requirements. The bylaws also include a similar requirement for making
nominations for directors. These provisions may preclude stockholders from
bringing matters before an annual meeting of stockholders or from making
nomination for directors at an annual or special meeting of stockholders.

TRANSFER AGENT AND REGISTRAR

    The transfer agent and registrar for the common stock is Boston EquiServe
L.P., Canton, Massachusetts.

                                       16
<PAGE>
                              PLAN OF DISTRIBUTION

    The shares covered by this prospectus may be offered and sold from time to
time by the selling stockholder. The term "selling stockholder" includes donees,
pledgees, transferees or other successors-in-interest selling shares received
after the date of this prospectus from the selling stockholder as a gift,
pledge, partnership distribution or other non-sale related transfer. The selling
stockholder will act independently of us in making decisions with respect to the
timing, manner and size of each sale. Such sales may be made on one or more
exchanges or in the over-the-counter market or otherwise, at prices and under
terms then prevailing or at prices related to the then current market price or
in negotiated transactions. The selling stockholder may sell its shares by one
or more of, or a combination of, the following methods:

    - purchases by a broker-dealer as principal and resale by such broker-dealer
      for its own account pursuant to this prospectus;

    - ordinary brokerage transactions and transactions in which the broker
      solicits purchasers;

    - block trades in which the broker-dealer so engaged will attempt to sell
      the shares as agent but may position and resell a portion of the block as
      principal to facilitate the transaction;

    - an over-the-counter distribution in accordance with the rules of the
      Nasdaq National Market;

    - in privately negotiated transactions; and

    - in options transactions.

    In addition, any shares that qualify for sale pursuant to Rule 144 may be
sold under Rule 144 rather than pursuant to this prospectus.

    To the extent required, this prospectus may be amended or supplemented from
time to time to describe a specific plan of distribution. In connection with
distributions of the shares or otherwise, the selling stockholder may enter into
hedging transactions with broker-dealers or other financial institutions. In
connection with such transactions, broker-dealers or other financial
institutions may engage in short sales of the common stock in the course of
hedging the positions they assume with the selling stockholder. The selling
stockholder may also sell the common stock short and redeliver the shares to
close out such short positions. The selling stockholder may also enter into
option or other transactions with broker-dealers or other financial institutions
which require the delivery to such broker-dealer or other financial institution
of shares offered by this prospectus, which shares such broker-dealer or other
financial institution may resell pursuant to this prospectus (as supplemented or
amended to reflect such transaction). The selling stockholder may also pledge
shares to a broker-dealer or other financial institution, and, upon a default,
such broker-dealer or other financial institution, may effect sales of the
pledged shares pursuant to this prospectus (as supplemented or amended to
reflect such transaction).

    In effecting sales, broker-dealers or agents engaged by the selling
stockholder may arrange for other broker-dealers to participate. Broker-dealers
or agents may receive commissions, discounts or concessions from the selling
stockholder in amounts to be negotiated immediately prior to the sale.

    In offering the shares covered by this prospectus, the selling stockholder
and any broker-dealers who execute sales for the selling stockholder may be
deemed to be "underwriters" within the meaning of the Securities Act in
connection with such sales. Any profits realized by the selling stockholder and
the compensation of any broker-dealer may be deemed to be underwriting discounts
and commissions.

    In order to comply with the securities laws of certain states, if
applicable, the shares must be sold in such jurisdictions only through
registered or licensed brokers or dealers. In addition, in certain states the
shares may not be sold unless they have been registered or qualified for sale in
the applicable state or an exemption from the registration or qualification
requirement is available and is complied with.

                                       17
<PAGE>
    We have advised the selling stockholder that the anti-manipulation rules of
Regulation M under the Exchange Act may apply to sales of shares in the market
and to the activities of the selling stockholder and its affiliates. In
addition, we will make copies of this prospectus available to the selling
stockholder for the purpose of satisfying the prospectus delivery requirements
of the Securities Act. The selling stockholder may indemnify any broker-dealer
that participates in transactions involving the sale of the shares against
certain liabilities, including liabilities arising under the Securities Act.

    At the time a particular offer of shares is made, if required, a prospectus
supplement will be distributed that will set forth the number of shares being
offered and the terms of the offering, including the name of any underwriter,
dealer or agent, the purchase price paid by any underwriter, any discount,
commission and other item constituting compensation, any discount, commission or
concession allowed or reallowed or paid to any dealer, and the proposed selling
price to the public.

    We have agreed to indemnify the selling stockholder against certain
liabilities, including certain liabilities under the Securities Act.

    We have agreed with the selling stockholder to keep the registration
statement of which this prospectus constitutes a part effective until the
earlier of (i) such time as all of the shares covered by this prospectus have
been disposed of pursuant to and in accordance with the registration statement
or (ii) six months from the date the registration statement is declared
effective.

                                       18
<PAGE>
                                    EXPERTS

    Ernst & Young LLP, independent auditors, have audited our consolidated
financial statements included in our Annual Report on Form 10-K for the year
ended December 31, 1999, as set forth in their report, which is incorporated by
reference in this prospectus and elsewhere in the registration statement. Our
financial statements are incorporated by reference in reliance on Ernst & Young
LLP's report, given on their authority as experts in accounting and auditing.

    The consolidated financial statements of LeukoSite, Inc. as of December 31,
1997 and 1998 and for each of the three years in the period ended December 31,
1998 and the financial statements of L&I Partners, L.P. as of December 31, 1997
and 1998 and for the period from inception through December 31, 1997, the year
ended December 31, 1998 and the period from inception through December 31, 1998
incorporated by reference in this prospectus and elsewhere in the registration
statement have been audited by Arthur Andersen LLP, independent public
accountants, as indicated in their reports with respect thereto, and are
included herein in reliance upon the authority of said firm as experts in giving
said reports.

    The financial statements of CytoMed, Inc. as of December 31, 1998 and 1997
and for each of the three years in the period ended December 31, 1998
incorporated in this prospectus by reference to the Millennium Pharmaceuticals
Form 8-K/A dated January 6, 2000, have been so incorporated in reliance on the
report of PricewaterhouseCoopers LLP, independent accountants, given on the
authority of said firm as experts in auditing and accounting.

                            VALIDITY OF COMMON STOCK

    The validity of the common stock offered hereby will be passed upon for us
by Hale and Dorr LLP, Boston, Massachusetts.

                      WHERE YOU CAN FIND MORE INFORMATION

    We file reports, proxy statements and other documents with the Securities
and Exchange Commission. You may read and copy any document we file at the SEC's
public reference room at Judiciary Plaza Building, 450 Fifth Street, N.W.,
Washington, D.C. 20549. You should call 1-800-SEC-0330 for more information on
the public reference room. The SEC maintains an Internet site that contains
reports, proxy and information statements and other information about issuers
that file electronically with the SEC. The address of the SEC's Internet site is
http://www.sec.gov.

    This prospectus is part of a registration statement that we filed with the
SEC. The registration statement contains more information than this prospectus
regarding us and our common stock, including certain exhibits and schedules. You
can obtain a copy of the registration statement from the SEC at the address
listed above or from the SEC's Internet site.

                INCORPORATION OF CERTAIN DOCUMENTS BY REFERENCE

    The SEC allows us to "incorporate" into this prospectus information that we
file with the SEC in other documents. This means that we can disclose important
information to you by referring to other documents that contain that
information. The information incorporated by reference is considered to be part
of this prospectus. Information contained in this prospectus and information
that we file with the SEC in the future and incorporate by reference in this
prospectus automatically updates and supersedes previously filed information. We
incorporate by reference the documents listed below and any future filings we
make with the SEC under Sections 13(a), 13(c), 14 or 15(d) of the Securities
Exchange Act of 1934, prior to the sale of all the securities covered by this
prospectus.

(1) Our Annual Report on Form 10-K for the year ended December 31, 1999;

                                       19
<PAGE>
(2) Our Current Report on Form 8-K/A filed with the SEC on January 6, 2000;

(3) Our Current Report on Form 8-K filed with the SEC on January 6, 2000;

(4) Our Current Report on Form 8-K filed with the SEC on January 11, 2000;

(5) Our Current Report on Form 8-K filed with the SEC on January 19, 2000;

(6) Our Current Report on Form 8-K/A filed with the SEC on January 27, 2000;

(7) Our Current Report on Form 8-K filed with the SEC on February 9, 2000; and

(8) All other reports filed pursuant to Section 13(a) or 15(d) of the Exchange
    Act since December 31, 1999.

    You may request, orally or in writing, a copy of these documents, which will
be provided to you at no cost, by contacting:

                               Investor Relations
                               Millennium Pharmaceuticals, Inc.
                               75 Sidney Street
                               Cambridge, MA 02139
                               Telephone: (617) 679-7000

                                       20
<PAGE>
                                    PART II

INFORMATION NOT REQUIRED IN PROSPECTUS

ITEM 14. OTHER EXPENSES OF ISSUANCE AND DISTRIBUTION.

    The following table sets forth the various expenses to be incurred in
connection with the registration of the securities being registered hereby, all
of which will be borne by Millennium Pharmaceuticals, Inc. All amounts shown are
estimates except the Securities and Exchange Commission registration fee.

<TABLE>
<S>                                                           <C>
SEC registration fee........................................  $ 3,163
Legal fees and expenses.....................................  $ 5,000
Accounting fees and expenses................................  $ 5,000
Miscellaneous...............................................  $ 1,837
                                                              -------
      Total Expenses........................................  $15,000
                                                              =======
</TABLE>

ITEM 15. INDEMNIFICATION OF DIRECTORS AND OFFICERS.

    Article Nine of the Registrant's Amended and Restated Certificate of
Incorporation (the "Restated Certificate of Incorporation") provides that no
director of the Registrant shall be personally liable for any monetary damages
for any breach of fiduciary duty as a director, except to the extent that the
Delaware General Corporation Law prohibits the elimination or limitation of
liability of directors for breach of fiduciary duty.

    Article Nine of the Restated Certificate of Incorporation provides that a
director or officer of the Registrant (a) shall be indemnified by the Registrant
against all expenses (including attorneys' fees), judgments, fines and amounts
paid in settlement incurred in connection with any litigation or other legal
proceeding (other than an action by or in the right of the Registrant) brought
against him by virtue of his position as a director or officer of the Registrant
if he acted in good faith and in a manner he reasonably believed to be in, or
not opposed to, the best interests of the Registrant, and, with respect to any
criminal action or proceeding, had no reasonable cause to believe his conduct
was unlawful and (b) shall be indemnified by the Registrant against all expenses
(including attorneys' fees) and amounts paid in settlement incurred in
connection with any action by or in the right of the Registrant brought against
him by virtue of his position as a director or officer of the Registrant if he
acted in good faith and in a manner he reasonably believed to be in, or not
opposed to, the best interests of the Registrant, except that no indemnification
shall be made with respect to any matter as to which such person shall have been
adjudged to be liable to the Registrant, unless a court determines that, despite
such adjudication but in view of all of the circumstances, he is entitled to
indemnification of such expenses. Notwithstanding the foregoing, to the extent
that a director or officer has been successful, on the merits or otherwise,
including, without limitation, the dismissal of an action without prejudice, he
is required to be indemnified by the Registrant against all expenses (including
attorneys' fees) incurred in connection therewith. Expenses shall be advanced to
a Director or officer at his request, provided that he undertakes to repay the
amount advanced if it is ultimately determined that he is not entitled to
indemnification for such expenses.

    Indemnification is required to be made unless the Registrant determines that
the applicable standard of conduct required for indemnification has not been
met. In the event of a determination by the Registrant that the director or
officer did not meet the applicable standard of conduct required for
indemnification, or if the Registrant fails to make an indemnification payment
within 60 days after such payment is claimed by such person, such person is
permitted to petition the court to make an independent determination as to
whether such person is entitled to indemnification. As a condition precedent to
the right of indemnification, the director or officer must give the Registrant
notice of the

                                      II-1
<PAGE>
action for which indemnity is sought and the Registrant has the right to
participate in such action or assume the defense thereof.

    Section 145 of the General Corporation Law of Delaware provides that a
corporation has the power to indemnify a director, officer, employee or agent of
the corporation and certain other persons serving at the request of the
corporation in related capacities against amounts paid and expenses incurred in
connection with an action or proceeding to which he is or is threatened to be
made a party by reason of such position, if such person shall have acted in good
faith and in a manner he reasonably believed to be in or not opposed to the best
interests of the corporation, and, in any criminal proceeding, if such person
had no reasonable cause to believe his conduct was unlawful; provided that, in
the case of actions brought by or in the right of the corporation, no
indemnification shall be made with respect to any matter as to which such person
shall have been adjudged to be liable to the corporation unless and only to the
extent that the adjudicating court determines that such indemnification is
proper under the circumstances.

    Millennium Pharmaceuticals, Inc. has purchased directors' and officers'
liability insurance which would indemnify its directors and officers against
damages arising out of certain kinds of claims which might be made against them
based on their negligent acts or omissions while acting in their capacity as
such.

ITEM 16. EXHIBITS

<TABLE>
<CAPTION>
       EXHIBIT
       NUMBER                                   DESCRIPTION
- ---------------------   ------------------------------------------------------------
<C>                     <S>
         4.1*           Amended and Restated Certificate of Incorporation of the
                        Registrant.
         4.2*           Amended and Restated By-Laws of the Registrant.
         4.3            Registration Rights Agreement dated March 6, 2000 between
                        the Registrant and Abgenix, Inc.
         5.1            Opinion of Hale and Dorr LLP.
        23.1            Consent of Ernst & Young LLP
        23.2            Consent of Arthur Andersen LLP
        23.3            Consent of PricewaterhouseCoopers LLP.
        23.4            Consent of Hale and Dorr LLP, included in Exhibit 5.1 filed
                        herewith.
        24.1            Power of Attorney (See page II-5 of this Registration
                        Statement).
</TABLE>

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

*   Incorporated by reference to the Registrant's Quarterly Report on
    Form 10-Q, filed June 20, 1996

    (File No. 0-28494).

ITEM 17. UNDERTAKINGS.

    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, as amended (the "Securities Act");

        (ii) To reflect in the prospectus any facts or events arising after the
    effective date of this 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 this
    Registration Statement. Notwithstanding the foregoing, any increase or
    decrease in the volume of securities offered (if the total dollar value of
    securities offered would not exceed that which was

                                      II-2
<PAGE>
    registered) and any deviation from the low or high end of the estimated
    maximum offering range may be reflected in the form of prospectus filed with
    the Commission pursuant to Rule 424(b) if, in the aggregate, the changes in
    volume and price represent no more than 20 percent change in the maximum
    aggregate offering price set forth in the "Calculation of Registration Fee"
    table in the effective Registration Statement; and

        (iii) To include any material information with respect to the plan of
    distribution not previously disclosed in this Registration Statement or any
    material change to such information in this Registration Statement;

PROVIDED, HOWEVER, that paragraphs (1)(i) and (1)(ii) do not apply if the
information required to be included is a post-effective amendment by those
paragraphs is contained in periodic reports filed by the Company pursuant to
Section 13 or Section 15(d) of the Securities Exchange Act of 1934, as amended
(the "Exchange Act"), that are incorporated by reference in this Registration
Statement.

    (2) That, for the purposes of determining any liability under the Securities
Act, each 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 the 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.

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

    Insofar as indemnification for liabilities arising under the Securities Act
may be permitted to directors, officers and controlling persons of the
Registrant pursuant to the indemnification provisions described herein, or
otherwise, the Registrant has been advised that in the opinion of the Securities
and Exchange Commission such indemnification is against public policy as
expressed in the Securities 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 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
Securities Act and will be governed by the final adjudication of such issue.

                                      II-3
<PAGE>
                                   SIGNATURES

    Pursuant to the requirements of the Securities Act of 1933, as amended, 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 Cambridge, Commonwealth of Massachusetts, on
March 31, 2000.

<TABLE>
<S>                                                    <C>  <C>
                                                       MILLENNIUM PHARMACEUTICALS, INC.

                                                       BY:  /S/ JOHN B. DOUGLAS III
                                                            -----------------------------------------
                                                            John B. Douglas III
                                                            GENERAL COUNSEL AND SECRETARY
</TABLE>

                        SIGNATURES AND POWER OF ATTORNEY

    We, the undersigned officers and directors of Millennium Pharmaceuticals,
hereby severally constitute and appoint Kevin P. Starr, John B. Douglas III and
David E. Redlick and each of them singly, our true and lawful attorneys with
full power to any of them, and to each of them singly, to sign for us and in our
names in the capacities indicated below the Registration Statement on Form S-3
filed herewith and any and all pre-effective and post-effective amendments to
said Registration Statement and any subsequent registration statement filed
pursuant to Rule 462(b) under the Securities Act of 1933, as amended, and to
file the same with all exhibits thereto, and the other documents in connection
therewith, with the Securities and Exchange Commission, and generally to do all
such things in our name and behalf in our capacities as officers and directors
to enable Millennium Pharmaceuticals to comply with the provisions of the
Securities Act of 1933, as amended, and all requirements of the Securities and
Exchange Commission, hereby ratifying and confirming our signatures as they may
be signed by our said attorneys, or any of them, to said Registration Statement
and any and all amendments thereto.

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

<TABLE>
<CAPTION>
                      SIGNATURE                                    TITLE                      DATE
                      ---------                                    -----                      ----
<C>                                                    <S>                             <C>
                                                       Chairman of the Board of
                    MARK J. LEVIN                        Directors and Chief
     -------------------------------------------         Executive Officer (Principal    March 31, 2000
                    Mark J. Levin                        Executive Officer)

                   KEVIN P. STARR                      Chief Financial Officer
     -------------------------------------------         (Principal Financial and        March 31, 2000
                   Kevin P. Starr                        Accounting Officer)

                 JOSHUA BOGER, PH.D.                   Director
     -------------------------------------------                                         March 31, 2000
                 Joshua Boger, Ph.d.

                EUGENE CORDES, PH.D.                   Director
     -------------------------------------------                                         March 31, 2000
                Eugene Cordes, Ph.d.
</TABLE>

                                      II-4
<PAGE>

<TABLE>
<CAPTION>
                      SIGNATURE                                    TITLE                      DATE
                      ---------                                    -----                      ----
<C>                                                    <S>                             <C>
                A. GRANT HEIDRICH III                  Director
     -------------------------------------------                                         March 31, 2000
                A. Grant Heidrich III

             RAJU S. KUCHERLAPATI, PH.D.               Director
     -------------------------------------------                                         March 31, 2000
             Raju S. Kucherlapati, Ph.d.

                ERIC S. LANDER, PH.D.                  Director
     -------------------------------------------                                         March 31, 2000
                Eric S. Lander, Ph.d.

           CHRISTOPHER K. MIRABELLI, PH.D.             Director
     -------------------------------------------                                         March 31, 2000
           Christopher K. Mirabelli, Ph.d.

            STEVEN C. WHEELWRIGHT, PH.D.               Director
     -------------------------------------------                                         March 31, 2000
            Steven C. Wheelwright, Ph.d.
</TABLE>

                                      II-5
<PAGE>
                                 EXHIBIT INDEX

<TABLE>
<CAPTION>
       EXHIBIT
       NUMBER                                   DESCRIPTION
- ---------------------                           -----------
<C>                     <S>
         4.1*           Amended and Restated Certificate of Incorporation of the
                        Registrant.
         4.2*           Amended and Restated By-Laws of the Registrant.
         4.3            Registration Rights Agreement dated March 6, 2000 between
                        the Registrant and Abgenix, Inc.
         5.1            Opinion of Hale and Dorr LLP.
        23.1            Consent of Ernst & Young LLP
        23.2            Consent of Arthur Andersen LLP
        23.3            Consent of PricewaterhouseCoopers LLP.
        23.4            Consent of Hale and Dorr LLP, included in Exhibit 5.1 filed
                        herewith.
        24.1            Power of Attorney (See page II-5 of this Registration
                        Statement).
</TABLE>

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

*   Incorporated by reference to the Registrant's Quarterly Report on
    Form 10-Q, filed June 20, 1996 (File No. 0-28494).

                                      II-6

<PAGE>

                                                                     Exhibit 4.3

         REGISTRATION RIGHTS AGREEMENT effective as of March 6, 2000 between
ABGENIX, INC., a Delaware corporation ("ABX"), having a place of business at
7601 Dumbarton Circle, Fremont, California 94555, and MILLENNIUM
PHARMACEUTICALS, INC., a Delaware corporation ("Millennium"), having a place of
business at 75 Sidney Street, Cambridge, Massachusetts 02139.


                                       1
<PAGE>

1.       REGISTRATION OF SHARES. Subject to reasonable cooperation by ABX,
within 10 days after each payment due date under Section 6.1 at which Millennium
elects to effect payment with Registrable Securities (20 days in the case of the
payment due date specified in Section 6.1.1), Millennium shall file with the
Securities and Exchange Commission ("SEC") a registration statement on Form S-3
(the "Registration Statement") covering the resale to the public by ABX of such
Registrable Securities. Millennium shall use its best efforts to cause the
Registration Statement to be declared effective by the SEC as soon as
practicable. Millennium shall cause the Registration Statement to remain
effective for a period of six (6) months (subject to extension pursuant to
Section 3 hereof) or until such earlier time as all of the Registrable
Securities shall have been sold pursuant thereto. The Registration Statement
shall not cover any securities other than the Registrable Securities unless (a)
otherwise agreed to by ABX or (b) Millennium is otherwise required to include
shares of Common Stock or other securities held by third parties pursuant to
existing and future contractual commitments of Millennium.

2.       REGISTRATION PROCEDURES.

         (a) In connection with the filing by Millennium of each Registration
Statement, Millennium shall:

         (1) before filing with the SEC the Registration Statement, furnish to
ABX and its counsel a draft thereof and provide them with a reasonable
opportunity for review thereof and comment thereon, such review to be conducted
and such comments to be delivered with reasonable promptness;

         (2) promptly (A) notify ABX of the filing and effectiveness thereof, of
the receipt of any comments from the SEC or any state securities law authorities
with respect thereto, of any oral or written stop order with respect thereto,
and of any suspension of the registration or qualification of the Registrable
Securities in any jurisdiction or any initiation or threatening of any
proceedings with respect to the foregoing, and (B) use its reasonable efforts to
obtain the withdrawal of any order suspending the registration or qualification
(or the effectiveness thereof) or suspending or preventing the use of any
related prospectus in any jurisdiction with respect thereto;

         (3) furnish to ABX a conformed copy of the Registration Statement and
each amendment and supplement thereto (in each case, including all exhibits
thereto and documents


                                       2
<PAGE>

incorporated by reference therein) and such additional number of copies of such
Registration Statement, each amendment and supplement thereto, the prospectus
(including each preliminary prospectus) included in the Registration Statement
and prospectus supplements and all exhibits thereto and documents incorporated
by reference therein and such other documents as ABX may reasonably request in
order to facilitate the disposition of the Registrable Securities;

         (4) if requested by ABX, subject to approval of counsel to Millennium,
promptly incorporate in a prospectus supplement or post-effective amendment to
the Registration Statement such information concerning the plan of distribution
of the Registrable Securities as ABX reasonably shall furnish to Millennium in
writing and request be included therein; and make all required filings of such
prospectus supplement or post-effective amendment as soon as reasonably possible
after being notified of the matters to be incorporated therein;

         (5) notify ABX, at any time when a prospectus relating to the
Registrable Securities is required to be delivered under the Securities Act
other than during a Blackout Period (as defined below), upon the discovery that,
or of the happening of any event as a result of which, the Registration
Statement as then in effect contains an untrue statement of a material fact or
omits to state any material fact required to be stated therein or any fact
necessary to make the statements therein not misleading, and promptly prepare
and furnish to ABX a supplement or amendment to the prospectus contained in the
Registration Statement so that the Registration Statement shall not, and such
prospectus as thereafter delivered to the purchaser of Registrable Securities
shall not, contain an untrue statement of a material fact or omit to state any
material fact required to be stated therein or any fact necessary to make the
statements therein not misleading;

         (6) cause all of the Registrable Securities to be listed on each
securities exchange and included in each Trading Market on which or through
which the securities of the same class of Millennium are then listed or traded;
and

         (7) make generally available to its security holders as soon as
practicable (but in any event not later than 90 days following the end of the
12-month period beginning at the end of the fiscal quarter during which the
effective date of the Registration Statement occurs) an earnings statement
(which need not be audited) of Millennium and its subsidiaries complying with
Section 11(a) of the Securities Act or Rule 158 promulgated by the SEC under the
Securities Act.

         (b) Millennium shall use its best efforts to register or qualify the
Registrable Securities covered by the Registration Statement under the
securities laws of each state of the


                                       3
<PAGE>

United States; provided, however, that Millennium shall not be required in
connection with this paragraph (b) to qualify as a foreign corporation or
execute a general consent to service of process in any jurisdiction.

         (c) If Millennium has delivered preliminary or final prospectuses to
ABX and after having done so the prospectus is amended or supplemented to comply
with the requirements of the Securities Act, Millennium shall promptly notify
ABX and, if requested by Millennium, ABX shall immediately cease making offers
or sales of shares under the Registration Statement and return all prospectuses
to Millennium. Millennium shall promptly provide ABX with revised or
supplemented prospectuses and, following receipt of the revised or supplemented
prospectuses, ABX shall be free to resume making offers and sales under the
Registration Statement.

         (d) Millennium shall pay the expenses incurred by it in complying with
its obligations under this Section 2, including all registration and filing
fees, exchange listing fees, blue sky fees and expenses, printing expenses, fees
and expenses of its counsel, and fees and expenses of its accountants, but
excluding (i) any brokerage fees, selling commissions or underwriting discounts
incurred by ABX in connection with sales under the Registration Statement and
(ii) the fees and expenses of any counsel retained by ABX.

3.       LIMITATIONS ON REGISTRATION RIGHTS.

         Millennium may, by written notice to ABX, (i) delay the filing or
effectiveness of a Registration Statement or (ii) suspend a Registration
Statement after effectiveness and require that ABX immediately cease sales of
shares pursuant to such Registration Statement, in either case for a reasonable
period of time (a "Blackout Period"), in the event that (A) Millennium files a
registration statement (other than a registration statement on Form S-4, Form
S-8 or their respective successor forms) with the SEC for a primary public
offering of its equity securities or securities convertible into or exercisable
for equity securities or (B) Millennium is engaged in any activity or
transaction or preparations or negotiations for any activity or transaction that
Millennium desires to keep confidential for business reasons, if Millennium
determines in good faith that the public disclosure requirements imposed on
Millennium under the Securities Act of 1933, as amended (the "Securities Act")
in connection with such Registration Statement would require disclosure of such
activity, transaction, preparations or negotiations.

         If Millennium delays or suspends a Registration Statement or requires
ABX to cease sales of shares pursuant to paragraph (a) above, Millennium shall,
as promptly as practicable


                                       4
<PAGE>

following the termination of the circumstance which entitled Millennium to do
so, take such actions as may be necessary to file or reinstate the effectiveness
of such Registration Statement and/or give written notice to ABX authorizing it
to resume sales pursuant to such Registration Statement. If as a result thereof
the prospectus included in a Registration Statement has been amended to comply
with the requirements of the Securities Act, Millennium shall enclose such
revised prospectus with the notice to ABX given pursuant to this paragraph (b),
and ABX shall make no offers or sales of shares pursuant to such Registration
Statement other than by means of such revised prospectus.

         Notwithstanding anything herein to the contrary, the aggregate number
of days included in any Blackout Periods with respect to each Registration
Statement shall not exceed 60 days, and the period of time that Millennium is
obligated to cause such Registration Statement to remain effective under Section
1 hereof shall be extended for a period of time equal to the number of days
included in such Blackout Periods.

4.       REQUIREMENTS OF ABX.

         (a) Millennium shall not be required to include any Registrable
Securities in the Registration Statement unless ABX furnishes to Millennium in
writing such information regarding it and the proposed sale of Registrable
Securities by ABX as Millennium may reasonably request in writing in connection
with the Registration Statement or as shall be required in connection therewith
by the SEC or any state securities law authorities.

         (b) ABX agrees to effect all sales of Registrable Securities through a
registered broker-dealer. ABX hereby covenants to promptly report to Millennium
in writing any sales made pursuant to the Registration Statement.

5.       INDEMNIFICATION.

         (a) Millennium will indemnify and hold harmless ABX, its officers,
directors, employees and agents and each person who controls ABX within the
meaning of Section 15 of the Securities Act from and against any and all losses,
claims, damages, expenses or liabilities, joint or several, to which they or any
of them become subject under the Securities Act, applicable state securities
laws or under any other statute or at common law or otherwise, as incurred, and,
except as hereinafter provided, will reimburse ABX and each such officer,
director, employee,


                                       5
<PAGE>

agent and controlling person for any legal or other expenses reasonably incurred
by them or any of them in connection with investigating or defending any actions
whether or not resulting in any liability, insofar as such losses, claims,
damages, expenses, liabilities or actions arise out of or are based upon any
untrue statement or alleged untrue statement of a material fact contained in the
Registration Statement, in any preliminary or amended preliminary prospectus or
in the final prospectus (or the Registration Statement or any such prospectus as
from time to time amended or supplemented by Millennium), or arise out of or are
based upon the omission or alleged omission to state therein a material fact
required to be stated therein or necessary in order to make the statements
therein, in the light of the circumstances in which they were made, not
misleading, or any violation by Millennium of the Securities Act or any rule or
regulations promulgated under the Securities Act or any state securities laws
applicable to Millennium and relating to action or inaction required of
Millennium in connection with such registration. Notwithstanding the foregoing,
Millennium shall have no obligation to indemnify ABX if: (i) such untrue
statement or omission was made in such Registration Statement, preliminary or
amended preliminary prospectus or final prospectus in reliance upon and in
conformity with information furnished in writing to Millennium in connection
therewith by ABX expressly for use therein, or (ii) such untrue statement or
alleged untrue statement or omission or alleged omission was contained in a
preliminary prospectus and corrected in a final or amended prospectus copies of
which were delivered to ABX on a timely basis, and ABX failed to deliver a copy
of the final or amended prospectus at or prior to the confirmation of the sale
of the Registrable Securities to the person asserting any such loss, claim,
damage or liability in any case where such delivery is required by the
Securities Act.

         (b) ABX will indemnify and hold harmless Millennium, each of its
directors, each of its officers who have signed or otherwise participated in the
preparation of the Registration Statement and each person, if any, who controls
Millennium within the meaning of Section 15 of the Securities Act from and
against any and all losses, claims, damages, expenses or liabilities, joint or
several, to which they or any of them may become subject under the Securities
Act, applicable state securities law or under any other statute or at common law
or otherwise, and, except as hereinafter provided, will reimburse Millennium and
each such director, officer, or controlling person for any legal or other
expenses reasonably incurred by them or any of them in connection with
investigating or defending any actions whether or not resulting in any
liability, insofar as such losses, claims, damages, expenses, liabilities or
actions arise out of or are based upon any untrue statement of a material fact
contained in the Registration Statement, in any preliminary or amended
preliminary prospectus or in the final prospectus (or in the Registration
Statement or any such prospectus as from time to time amended or supplemented)
or arise out of or are based upon the omission to state therein a material fact
required to be stated therein or necessary in order to make the statements
therein not misleading, but only to the extent that such statement or omission
was made in reliance upon and in conformity with information furnished in
writing to Millennium in connection therewith by ABX expressly for use therein.
Notwithstanding the foregoing, the liability of ABX under this paragraph (b)
shall not exceed the proceeds received by ABX from the sale of Registrable
Securities pursuant to the Registration Statement.


                                       6
<PAGE>

         (c) In order to provide for just and equitable contribution to joint
liability under the Securities Act in any case in which Millennium or ABX makes
a claim for indemnification pursuant to this Section 5 but it is judicially
determined (by the entry of a final judgment or decree by a court of competent
jurisdiction and the expiration of time to appeal or the denial of the last
right of appeal) that such indemnification may not be enforced in such case
notwithstanding that this Section 5 provides for indemnification, in such case,
then Millennium and ABX will contribute to the aggregate losses, claims, damages
or liabilities to which they may be subject (after contribution from others) in
such proportion as is appropriate to reflect the relative fault of Millennium on
the one hand and of ABX on the other in connection with the statements or
omission which resulted in such losses, claims, damages or liabilities, as well
as any other relevant equitable considerations or, if the allocation provided
herein is not permitted by applicable law, in such proportion as shall be
appropriate to reflect the relative benefits received by Millennium and ABX from
the offering of the securities covered by such Registration Statement. The
relative fault of Millennium on the one hand and of ABX on the other shall be
determined by reference to, among other things, whether the untrue or alleged
untrue statement of a material fact or omission or alleged omission to state a
material fact relates to information supplied by Millennium on the one hand or
by ABX on the other, and each party's relative intent, knowledge, access to
information and opportunity to correct or prevent such statement or omission;
provided, however, that, in any such case (i) ABX will not be required to
contribute any amount in excess of the proceeds received by ABX from the sale of
Registrable Securities offered by it pursuant to the Registration Statement; and
(ii) no person or entity guilty of fraudulent misrepresentation within the
meaning of Section 11(f) of the Securities Act will be entitled to contribution
from any person or entity who was not guilty of such fraudulent
misrepresentation.

         (d) Each person entitled to indemnification under this Section 5 (an
"Indemnitee") shall give notice to the party required to provide indemnification
(the "Indemnitor") promptly after such Indemnitee has actual knowledge of any
claim as to which indemnity may be sought, and the Indemnitor shall assume the
defense of any such claim and any litigation resulting therefrom, including the
employment of counsel selected by the Indemnitor (and reasonably acceptable to
the Indemnitee) and shall assume the payment of all expenses. The Indemnitee
shall have the right to employ separate counsel in any such action and to
participate in the defense thereof, but the fees and expenses of such counsel
shall be at the expense of such Indemnitee, except that the Indemnitor shall pay
the fees and expenses of such counsel if counsel retained by the Indemnitor
reasonably determines that dual representation would be inadvisable due to
actual or potential differing interests between the parties. The failure of any
Indemnitee to give notice as provided herein shall not relieve the Indemnitor of
its obligations under this Section 5.3.5 except to the extent the Indemnitor is
materially prejudiced thereby. The Indemnitor shall not be liable for any
settlement of any such action or proceedings effected without its written
consent, but if settled with its written consent, or if there be a final
judgment for the plaintiff in any such action or proceeding, the Indemnitor
shall indemnify and hold harmless such Indemnitee from and against any loss or
liability (to the extent stated above) by


                                       7
<PAGE>

reason of such settlement or judgment. Each Indemnitee shall furnish such
information regarding itself or the claim in question as an Indemnitor may
reasonably request in writing and as shall be reasonably required in connection
with the defense of such claim and litigation resulting therefrom.

6. LEGENDS . Each certificate representing Registrable Securities initially
shall bear a legend substantially in the following form:

                  "The shares represented by this certificate have not been
                  registered under the Securities Act of 1933, as amended, and
                  may not be offered, sold or otherwise transferred, pledged or
                  hypothecated, other than to a wholly-owned subsidiary of the
                  holder or pursuant to Rule 144 under such Act, unless and
                  until such shares are registered under such Act or an opinion
                  of counsel satisfactory to Millennium Pharmaceuticals, Inc. is
                  obtained to the effect that such registration is not
                  required."

The foregoing legend shall be removed from the certificates representing any
Registrable Securities, at the request of the holder thereof, at such time as
they become (a) subject to a Registration Statement declared effective under the
Securities Act, or (b) eligible for resale pursuant to Rule 144(k) under the
Securities Act.

7.       RULE 144 INFORMATION. With a view to making available to ABX the
benefits of Rule 144 under the Securities Act and any other rule or regulation
of the SEC that may at any time permit ABX to sell Registrable Securities to the
public without registration, Millennium agrees that it shall, at all times from
the date hereof until all of the Registrable Securities shall have been sold by
ABX:

         (a) make and keep available adequate current public information, as
those terms are understood and defined in Rule 144 under the Securities Act;

         (b) use its best efforts to file with the SEC in a timely manner all
reports and other documents required to be filed by Millennium under the
Securities Act and the Securities Exchange Act of 1934, as amended (the
"Exchange Act"); and


                                       8
<PAGE>

         (c) furnish to ABX, promptly upon request, a written statement by
Millennium as to its compliance with the reporting requirements of Rule 144 and
of the Securities Act and the Exchange Act, a copy of the most recent annual or
quarterly report of Millennium, and such other reports and documents of
Millennium and other information in the possession of or reasonably obtainable
by Millennium as ABX may reasonably request in availing itself of any rule or
regulation of the SEC allowing ABX to sell any such securities without
registration.


                                       9

<PAGE>


                                                                     Exhibit 5.1

                                HALE AND DORR LLP
                               COUNSELLORS AT LAW
                  60 STATE STREET, BOSTON, MASSACHUSETTS 02109
                         617-526-6000 - FAX 617-526-5000

                                 March 31, 2000

Millennium Pharmaceuticals, Inc.
75 Sidney Street
Cambridge, MA 02139

REGISTRATION STATEMENT ON FORM S-3

Ladies and Gentlemen:

         This opinion is furnished to you in connection with a Registration
Statement on Form S-3 (the "Registration Statement") to be filed with the
Securities and Exchange Commission (the "Commission") under the Securities Act
of 1933, as amended (the "Securities Act"), for the registration of an aggregate
of 81,800 shares of Common Stock, $.001 par value per share (the "Shares"), of
Millennium Pharmaceuticals, Inc., a Delaware corporation (the "Company"). All of
the Shares are being registered on behalf of a certain stockholder of the
Company (the "Selling Stockholder").

         We have acted as counsel for the Company in connection with the
registration for resale of the Shares. We have examined signed copies of the
Registration Statement to be filed with the Commission. We have also examined
and relied upon the minutes of meetings of the stockholders and the Board of
Directors of the Company as provided to us by the Company, stock record books of
the Company as provided to us by the Company, the Certificate of Incorporation
and By-Laws of the Company, each as restated and/or amended to date, and such
other documents as we have deemed necessary for purposes of rendering the
opinions hereinafter set forth.

         In our examination of the foregoing documents, we have assumed the
genuineness of all signatures, the authenticity of all documents submitted to us
as originals, the conformity to original documents of all documents submitted to
us as copies, the authenticity of the originals of such latter documents and the
legal competence of all signatories to such documents.

         We assume that the appropriate action will be taken, prior to the offer
and sale of the Shares, to register and qualify the Shares for sale under all
applicable state securities or "blue sky" laws.

         We express no opinion herein as to the laws of any state or
jurisdiction other than the state laws of the Commonwealth of Massachusetts, the
Delaware General Corporation Law and the federal laws of the United States of
America.

         Based upon and subject to the foregoing, we are of the opinion that the
Shares have been duly authorized and are validly issued, fully paid and
nonassessable.

         It is understood that this opinion is to be used only in connection
with the offer and sale of the Shares while the Registration Statement is in
effect.

         Please note that we are opining only as to the matters expressly set
forth herein, and no opinion should be inferred as to any other matters.


<PAGE>

         We hereby consent to the filing of this opinion with the Commission as
an exhibit to the Registration Statement in accordance with the requirements of
Item 601(b)(5) of Regulation S-K under the Securities Act and to the use of our
name therein and in the related prospectus under the caption "Validity of Common
Stock." In giving such consent, we do not hereby admit that we are in the
category of persons whose consent is required under Section 7 of the Securities
Act or the rules and regulations of the Commission.

                                                     Very truly yours,

                                                     /s/ HALE AND DORR LLP

                                                     HALE AND DORR LLP

<PAGE>
                                                                    EXHIBIT 23.1

                        CONSENT OF INDEPENDENT AUDITORS

    We consent to the reference to our firm under the caption "Experts" in the
Registration Statement (Form S-3) and related Prospectus of Millennium
Pharmaceuticals, Inc. for the registration of 81,800 shares of its common stock
and to the incorporation by reference therein of our report dated January 27,
2000, with respect to the consolidated financial statements of Millennium
Pharmaceuticals, Inc. included in its Annual Report (Form 10-K) for the year
ended December 31, 1999, filed with the Securities and Exchange Commission.

                                          /s/ Ernst & Young LLP

Boston, Massachusetts
March 29, 2000

<PAGE>
                                                                    EXHIBIT 23.2

                   CONSENT OF INDEPENDENT PUBLIC ACCOUNTANTS

    As independent public accountants, we hereby consent to the incorporation by
reference in this Registration Statement of our report dated January 29, 1999
for LeukoSite, Inc. financial statements as of December 31, 1997 and 1998 and
for the three years in the period ended December 31, 1998 and to all references
to our Firm included in or made part of this Registration Statement.

                                                         /s/ ARTHUR ANDERSEN LLP

Boston, Massachusetts
March 31, 2000

<PAGE>
                                                                    EXHIBIT 23.3

                       CONSENT OF INDEPENDENT ACCOUNTANTS

    We hereby consent to the incorporation by reference in this Registration
Statement on Form S-3 of Millennium Pharmaceuticals, Inc. of our report dated
February 12, 1999 relating to the financial statements of CytoMed, Inc., which
appears in the Current Report on Form 8-K/A of Millennium Pharmaceuticals, Inc.
dated January 6, 2000. We also consent to the reference to us under the heading
"Experts" in such Registration Statement.

                                                      PRICEWATERHOUSECOOPERS LLP

Boston, Massachusetts
March 29, 2000


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