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                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

                                    FORM 10-Q

        x QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES
          EXCHANGE ACT OF 1934

       For the quarterly period ended March 31, 1999

       OR

       _ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES
         EXCHANGE ACT OF 1934

             For the transition period from __________ to __________

                         COMMISSION FILE NUMBER 0-28494

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

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

                     640 MEMORIAL DRIVE, CAMBRIDGE, MA 02139
          (Address of principal executive offices, including zip code)

                                  617-679-7000
              (Registrant's telephone number, including area code)

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

Number of shares of Common Stock, $.001 par value per share, outstanding as of
May 10, 1999 was 35,776,682.

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                        MILLENNIUM PHARMACEUTICALS, INC.
                               REPORT ON FORM 10-Q
                  FOR THE QUARTERLY PERIOD ENDED MARCH 31, 1999

                                TABLE OF CONTENTS

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                                                                                      PAGE
                                                                                      ----
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         PART I -    FINANCIAL INFORMATION

         ITEM 1.     FINANCIAL STATEMENTS (unaudited)

                     Condensed Consolidated Balance Sheets                              3
                        March 31, 1999 and December 31, 1998

                     Condensed Consolidated Statements of Operations and
                     Comprehensive Income (Loss) for the three months
                        ended March 31, 1999 and 1998                                   4

                     Condensed Consolidated Statements of Cash Flows
                        for the three months ended March 31, 1999 and 1998              5
                       
                     Notes to Condensed Consolidated Financial Statements               6

         ITEM 2.     MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL                
                     CONDITION AND RESULTS OF OPERATIONS                                7

         PART II -   OTHER INFORMATION                                                 11
         ITEM 6.     EXHIBITS AND REPORTS ON FORM 8-K                                  11

         SIGNATURES                                                                    12
         EXHIBIT INDEX                                                                 13
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                        Millennium Pharmaceuticals, Inc.
                      CONDENSED CONSOLIDATED BALANCE SHEETS

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<CAPTION>
                                                                              MARCH 31,             DECEMBER 31,
(in thousands, except par value and shares)                                     1999                  1998
                                                                             -----------------------------------
                                                                             (Unaudited)             (Note)
<S>                                                                          <C>                   <C>
ASSETS
Current assets:
Cash and cash equivalents                                                     $  84,923             $ 138,284
Marketable securities                                                           138,049                52,680
Due from strategic partners                                                       3,323                 6,660
Prepaid expenses and other current assets                                         7,048                 5,033
                                                                              --------------------------------
Total current assets                                                            233,343               202,657

Property and equipment, net                                                      40,698                38,170
Restricted cash and other assets                                                 11,232                11,416
Intangible asset, net                                                             5,035                 5,711
                                                                              --------------------------------
Total assets                                                                  $ 290,308             $ 257,954
                                                                              ================================
LIABILITIES AND STOCKHOLDERS' EQUITY 
Current liabilities:
Accounts payable                                                              $   8,878             $   6,918
Accrued expenses                                                                  7,353                 6,186
Deferred revenue                                                                  6,316                 2,501
Current portion of capital lease obligations                                      8,227                 8,657
                                                                              --------------------------------
Total current liabilities                                                        30,774                24,262
Capital lease obligations, net of current portion                                25,970                24,827
Minority interest                                                                15,254                 2,503
Commitments and contingencies

Stockholders' equity:
Preferred Stock, $0.001 par value; 5,000,000 shares authorized:
none issued                                                                          --                    --
Common Stock, $0.001 par value: 100,000,000 shares authorized:
35,622,319 shares in 1999 and 34,923,204 shares in 1998 issued and
outstanding                                                                          36                    35
Additional paid-in capital                                                      306,185               296,370
Deferred compensation                                                              (751)                 (957)
Notes receivable from officers                                                      (68)                  (87)
Other comprehensive income (loss)                                                  (136)                   29
Accumulated deficit                                                             (86,956)              (89,028)
                                                                              --------------------------------
Total stockholders' equity                                                      218,310               206,362
                                                                              --------------------------------
Total liabilities and stockholders' equity                                    $ 290,308             $ 257,954
                                                                              ================================
</TABLE>

Note: The balance sheet at December 31, 1998 has been derived from the audited
financial statements at that date but does not include all of the information
and footnotes required by generally accepted accounting principles for complete
financial statements. 
See notes to condensed consolidated financial statements.

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                        Millennium Pharmaceuticals, Inc.
               CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS AND
                     COMPREHENSIVE INCOME (LOSS) (UNAUDITED)


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<CAPTION>
THREE MONTHS ENDED MARCH 31,                                     1999                    1998
(in thousands, except per share and share data)
--------------------------------------------------------------------------------------------------
<S>                                                         <C>                      <C>
Revenue under strategic alliances                           $     40,992             $     21,043

Costs and expenses:
   Research and development                                       35,433                   22,429
   General and administrative                                      7,126                    5,911
   Amortization of intangible asset                                  676                      675
                                                            --------------------------------------
                                                                  43,235                   29,015
                                                            --------------------------------------
Loss from operations                                              (2,243)                  (7,972)

Interest income                                                    2,759                    1,447
Interest expense                                                    (697)                    (645)
Minority interest                                                  2,253                    2,744
                                                            --------------------------------------
Net income (loss)                                           $      2,072             $     (4,426)
                                                            ======================================
Unrealized loss on marketable securities                            (165)                     (38)
                                                           
Comprehensive income (loss)                                 $      1,907             $     (4,464)
                                                            ======================================

Basic net income (loss) per share                           $       0.06             $      (0.15)

Shares used in computing basic net income (loss)
   per share                                                  35,315,034               29,262,189

Diluted net income (loss) per share                         $       0.05             $      (0.15)

Shares used in computing diluted net income
(loss) per share                                              38,193,493               29,262,189
                                                            ======================================
</TABLE>

See notes to condensed consolidated financial statements.

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                        Millennium Pharmaceuticals, Inc.
           CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS (UNAUDITED)

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<CAPTION>
THREE MONTHS ENDED MARCH 31,                                      1999                 1998
(in thousands)
-----------------------------------------------------------------------------------------------
<S>                                                            <C>                   <C>
CASH PROVIDED BY (USED IN) OPERATIONS                          $  13,037             $  (6,748)

INVESTING ACTIVITIES
Purchase of property and equipment                                (3,778)               (3,512)
Sale of marketable securities                                     15,500                15,395
Purchase of marketable securities                               (101,034)              (24,039)
                                                               --------------------------------
Net cash used in investing activities                            (89,312)              (12,156)

FINANCING ACTIVITIES
Proceeds from sale of subsidiary stock                            15,000                    --
Net proceeds from employee stock purchases                         9,817                 1,498
Repurchase of Common Stock                                            (1)                   (3)
Payments of capital lease obligations                             (1,902)               (1,532)
                                                               --------------------------------
Net cash provided by (used in) financing activities               22,914                   (37)
                                                               --------------------------------
Decrease in cash and cash equivalents                            (53,361)              (18,941)
Cash and cash equivalents at beginning of period                 138,284                69,236
                                                               --------------------------------
Cash and cash equivalents at end of period                     $  84,923             $  50,295
                                                               ================================
NONCASH INVESTING AND FINANCING ACTIVITIES:
Equipment acquired under capital leases                        $   2,615             $   1,949
                                                               ================================
</TABLE>

See notes to condensed consolidated financial statements.

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                        MILLENNIUM PHARMACEUTICALS, INC.

              NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

                                 MARCH 31, 1999
                                   (unaudited)

1-       BASIS OF PRESENTATION

         The accompanying condensed consolidated financial statements have been
prepared in accordance with generally accepted accounting principles for interim
financial information and with the instructions to Form 10-Q and Article 10 of
Regulation S-X. Accordingly, they do not include all of the information and
footnotes required by generally accepted accounting principles for complete
financial statements. In the opinion of management, all adjustments (consisting
of normal recurring accruals) considered necessary for a fair presentation have
been included. Interim results for the three month period ended March 31, 1999
are not necessarily indicative of the results that may be expected for the year
ended December 31, 1999. For further information, refer to the financial
statements and footnotes thereto included in the Company's Annual Report on Form
10-K for the fiscal year ended December 31, 1998 which was filed with the
Securities Exchange Commission on March 24, 1999.

         In June 1998, the FASB issued SFAS No. 133, "Accounting for Derivative
Instruments and Hedging Activities", which is effective for fiscal years
beginning after June 15, 1999. The Company believes the adoption of this new
accounting standard will not have a significant effect to its financial
statements as the Company's investment policies prohibit the use of derivatives.

2 -      STRATEGIC ALLIANCE

         On February 22, 1999, the Company announced the formation of a
strategic alliance in the diagnostic field between its wholly-owned subsidiary,
Millennium Predictive Medicine, Inc. ("MPMx") and Becton, Dickinson and Company
("Becton Dickinson"). The five-year, genomics-based research collaboration will
focus on several areas of oncology.

         Under the alliance, MPMx has agreed to undertake a research program to
identify genetic markers and related assays that may be used to develop
diagnostic products for several types of cancer. Becton Dickinson has agreed to
manufacture and market any products that result, and MPMx will receive a royalty
based upon gross profits from related product sales.

         On March 31, 1999, Becton Dickinson made an equity investment in MPMx
of $15 million, representing approximately an 11% voting interest in MPMx, and
paid a $3 million licensing fee to MPMx. Becton Dickinson has agreed to pay MPMx
up to $51.5 million in research funding and additional annual license fees, over
the five-year term. Becton Dickinson has agreed to pay milestones and royalties
to MPMx in connection with the commercialization and sale of any products
developed through the alliance.

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ITEM 2.  MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS
         OF OPERATIONS.

         This Report on Form 10-Q contains forward-looking statements. For this
purpose, any statements contained herein that are not statements of historical
fact may be deemed to be forward-looking statements. Without limiting the
foregoing, the words "believes," "anticipates," "plans," "expects," "intends,"
and similar expressions are intended to identify forward-looking statements.
There are a number of important factors that could cause the Company's actual
results to differ materially from those indicated by such forward-looking
statements. These factors are set forth under the caption "Factors That May
Affect Results" in the Company's Annual Report on Form 10-K for the year ended
December 31, 1998, which "Factors That May Affect Results" discussion is
expressly incorporated by reference herein.

Overview

         Millennium Pharmaceuticals, Inc. ("Millennium" or the "Company"), was
founded in 1993 and is applying a comprehensive integrated science and
technology platform which incorporates large-scale genetics, genomics, high
throughput screening, and informatics. We apply this technology platform
primarily in discovering and developing proprietary therapeutic and diagnostic
human healthcare products and services. As used herein, the terms "the Company"
and "Millennium" include the Company's subsidiaries where appropriate in the
context.

Results of Operations

         Quarters Ended March 31, 1999 and March 31, 1998

         Revenue under strategic alliances increased to $40.9 million for the
three months ended March 31, 1999 (the "1999 Quarterly Period") from $21.0
million for the three months ended March 31, 1998 (the "1998 Quarterly Period").
The increase in revenue in the 1999 Quarterly Period is due primarily to revenue
from research funding and license fees under the Company's alliances with Bayer
AG ("Bayer") and Becton, Dickinson and Company ("Becton Dickinson"). Neither of
these alliances was in place during the 1998 Quarterly Period.

         Research and development expenses increased to $35.4 million for the
1999 Quarterly Period from $22.4 million for the 1998 Quarterly Period. The
increase was primarily attributable to increased personnel expenses, facilities
expenses, increases in spending for laboratory supplies and external
collaborations, and increased equipment depreciation. We expect research and
development expenses to continue to increase as personnel are added and as
research and development activities are expanded to accommodate our existing
strategic alliances and additional commitments that we may undertake in the
future.

         General and administrative expenses increased to $7.1 million for the
1999 Quarterly Period from $5.9 million for the 1998 Quarterly Period. The
increase was attributable primarily

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to increased personnel expenses as the Company has hired additional management,
business development, and administrative personnel. We expect that general and
administrative expenses will continue to increase as Millennium continues to
grow.

         The Company's total operating expenses increased to $43.2 million for
the 1999 Quarterly Period from $29.0 million for the 1998 Quarterly Period, for
the reasons discussed above with respect to the increase in research and
development and general and administrative expenses.

         Interest income was $2.8 million for the 1999 Quarterly Period and $1.4
million for the 1998 Quarterly Period. The increase resulted from an increase in
the Company's average balance of cash, cash equivalents and marketable
securities. Interest expense increased to $.7 million for the 1999 Quarterly
Period from $.6 million for the 1998 Quarterly Period due to increased capital
lease obligations.

         Minority interest represents the minority shareholder interest of Eli
Lilly and Company ("Lilly") in the net income or loss for the 1999 and 1998
Quarterly Periods of the Company's majority-owned subsidiary, Millennium
BioTherapeutics, Inc. ("MBio") as well as the minority shareholder interest of
Becton Dickinson in the net income or loss for the 1999 Quarterly Period of the
Company's majority-owned subsidiary, MPMx.

Liquidity and Capital Resources

         Since inception, the Company has recognized approximately $327.2
million of revenue under strategic alliances. As of March 31, 1999, the Company
had approximately $223.0 million in cash, cash equivalents and marketable
securities. This excludes $9.8 million of interest-bearing marketable securities
classified as restricted cash and other assets on the balance sheet which serve
as collateral for the Company's letters of credit.

         During the three months ended March 31, 1999, $13 million of cash was
provided by the Company's operations, we purchased $3.8 million of property and
equipment, and used cash of $1.9 million to pay capital lease obligations. In
addition, during the three months ended March 31, 1999, the Company acquired
equipment under capital leases of $2.6 million and received proceeds from
employee stock purchases of $9.8 million.

         The Company believes that existing cash and marketable securities and
anticipated cash payments from its strategic alliances will be sufficient to
support the Company's operations for the foreseeable future.

Year 2000

IMPACT OF YEAR 2000

The Year 2000 issue is the result of computer programs that were written using
two digits rather than four to define the applicable year. Any computer program
that has date-sensitive software may recognize a date using "00" as the year
1900 rather than the year 2000. It is possible that

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this incorrect recognition of dates could cause system failures or
miscalculations of data. If these errors were to occur in Millennium systems,
they could cause us to be unable to process data and engage in normal business
activities.

Millennium has determined that we have Year 2000 exposure in the following
areas: (i) software and hardware embedded in our laboratory equipment and used
in our research and development programs, (ii) computer software and hardware
used in our business and facilities operations and (iii) computer systems used
by vendors and suppliers with whom we do business. In addition, we have Year
2000 exposure with respect to internally developed informatics application
software that is used by Millennium and certain alliance partners who have
access to our technology platform.

Millennium has a Year 2000 task force that is evaluating our internal computer
programs, systems and equipment and overseeing our Year 2000 efforts. We are
using both internal and external resources to identify potential issues, costs
and solutions to address Year 2000 concerns. For this effort, we are using
procedures outlined in the Government Accounting Office's Y2K Guide. We have
completed a preliminary inventory of our informatics applications, and we are
conducting an in-depth assessment of this inventory. In addition, we have
inventoried a substantial amount of software and hardware embedded in our
laboratory and facilities equipment as part of our effort to determine Year 2000
compliance. We are also making inquiries of our important suppliers and vendors
to assess their Year 2000 readiness. We have inventoried software used in our
business operations as well. We intend to identify critical systems and
equipment on which to focus our inquiries and testing.

To date, we have identified aspects of our computer hardware, network
infrastructure and business systems that are not Year 2000 compliant. We have
obtained and begun to implement vendor recommendations for correcting these
deficiencies. We have also identified aspects of internally developed software
applications that are not Year 2000 compliant and have begun testing and
corrective programs in this area. We expect to complete testing and remediation
for critical computer hardware, network infrastructure, business systems and
internally developed software applications by the end of the third quarter of
1999.

We completed an initial inventory and preliminary risk assessment of critical
laboratory and facilities equipment and systems during first quarter of 1999. We
have obtained and are reviewing vendor provided documentation for these items.
We expect to complete testing and any remediation of critical laboratory and
facilities equipment by the end of the year.

There can be no assurance that we will not find problems that will require us to
incur substantial costs to correct or will disrupt our business. Should such
problems occur, they could have a material adverse effect on our business,
financial position or results of operations. At the current time, we expect to
be able to correct the problems of which we are aware in a reasonable and timely
manner. We are not experiencing and do not anticipate any forward-looking
problems.

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We do not currently have contingency plans for all critical aspects of our
systems and operations in the event that we or any of our important suppliers or
vendors are not able to become Year 2000 compliant. We expect to develop
contingency plans for critical areas if we determine that we or any important
vendors or suppliers are not likely to become Year 2000 compliant.

We have not incurred material remediation costs to date and we do not currently
expect that the aggregate cost of our efforts will be material to our operations
or financial position taken as a whole. However, it is possible that remediation
costs will be greater than we anticipate and that such costs could have a
material adverse effect on our financial position or results of operations. Our
alliance partners or collaborators may also experience disruption as a result of
the Year 2000 issue. If our alliance partners and collaborators experience
disruption, it is possible that our alliances with these partners could be
adversely affected, which could have a material adverse effect on our financial
position and results of operations.

There can be no assurance that we will identify all Year 2000 compliance
problems as a result of our efforts or that we will be able to correct
compliance problems that are identified in a timely manner. If we are unable, in
a timely manner, to identify and correct compliance problems in critical systems
and equipment, our business, financial position and results of operations could
be adversely affected.

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                           PART II - OTHER INFORMATION

Item 6.        Exhibits and Reports on Form 8-K.

      (a)      Exhibits

               The exhibits listed in the Exhibit Index are included in this
               report.

      (b)      Reports on Form 8-K

               The following current reports on Form 8-K were filed by the
               Company during the last quarter:

               1. Current Report on Form 8-K filed with the Securities and
                  Exchange Commission on March 11, 1999.

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              SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the
registrant has duly caused this report to be signed on its behalf by the
undersigned thereunto duly authorized.

                                  MILLENNIUM PHARMACEUTICALS, INC.
                                            (Registrant)

Date: May 12, 1999             By:   /s/ Kevin P. Starr
          -------                    ------------------------------------------
                                            Kevin P. Starr
                                            Chief Financial Officer
                                            (Principal Financial and Accounting
                                            Officer)

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                                  EXHIBIT INDEX

      The following exhibits are filed as part of this Quarterly Report on Form
10-Q:

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Exhibit
  No.               Description
  ---               -----------
<S>                 <C>
27.1                Financial Data Schedule for the quarter ended March 31, 1999

99.1                Pages 45 through 59 of the Company's Annual Report of Form
                    10-K for the year ended December 31, 1998, as filed with the
                    Securities Exchange Commission (which are deemed filed except to
                    the extent that portions are not expressly incorporated by reference
                    herein).
</TABLE>

+ Confidential treatment requested with respect to certain portions

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