<PAGE>   1


                       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 June 30, 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)


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


                      75 SIDNEY STREET, 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
July 26, 1999 was 36,201,748.


                                       1

<PAGE>   2

                        MILLENNIUM PHARMACEUTICALS, INC.
                               REPORT ON FORM 10-Q
                  FOR THE QUARTERLY PERIOD ENDED JUNE 30, 1999

                                TABLE OF CONTENTS


                                                                          PAGE
PART I - FINANCIAL INFORMATION

ITEM 1.     FINANCIAL STATEMENTS (unaudited)
            Condensed Consolidated Balance Sheets
              June 30, 1999 and December 31, 1998                          3

            Condensed Consolidated Statements of Operations
              for the three and six months ended June 30, 1999 and 1998    4

            Condensed Consolidated Statements of Cash Flows
              for the six months ended June 30, 1999 and 1998              5

            Notes to Condensed Consolidated Financial Statements           6

ITEM 2.     MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL              8
            CONDITION AND RESULTS OF OPERATIONS

ITEM 3.     QUALITATIVE AND QUANTITATIVE DISCLOSURE ABOUT MARKET RISK     14

ITEM 4.     SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS           14

PART II -   OTHER INFORMATION                                             15
ITEM 6.     EXHIBITS AND REPORTS ON FORM 8-K                              15

SIGNATURES                                                                16
EXHIBIT INDEX                                                             17



                                       2

<PAGE>   3


<TABLE>
<CAPTION>

                             MILLENNIUM PHARMACEUTICALS, INC.
                           CONDENSED CONSOLIDATED BALANCE SHEETS


                                                                   JUNE 30,     DECEMBER 31,
(IN THOUSANDS, EXCEPT PER SHARE AMOUNTS)                             1999          1998
                                                                 ----------     ------------
                                                                 (Unaudited)
<S>                                                               <C>            <C>
ASSETS
Current assets:
   Cash and cash equivalents                                      $  40,447      $ 138,284
   Marketable securities                                            175,465         52,680
   Due from strategic partners                                       13,879          6,660
   Prepaid expenses and other current assets                          7,179          5,033
                                                                  ---------      ---------
Total current assets                                                236,970        202,657

Property and equipment, net                                          49,004         38,170
Restricted cash and other assets                                     12,408         11,416
Intangible asset, net                                                 4,359          5,711
                                                                  ---------      ---------
Total assets                                                      $ 302,741      $ 257,954
                                                                  =========      =========

LIABILITIES AND STOCKHOLDERS' EQUITY
Current liabilities:
   Accounts payable                                               $  13,227      $   6,918
   Accrued expenses                                                   8,523          6,186
   Deferred revenue                                                   8,416          2,501
   Current portion of capital lease obligations                       8,514          8,657
                                                                  ---------      ---------
Total current liabilities                                            38,680         24,262

Capital lease obligations, net of current portion                    25,466         24,827
Minority interest                                                    15,220          2,503
Commitments and contingencies
Stockholders' equity:
   Preferred Stock, $0.001 par value; 5,000 shares
   authorized:  none issued
   Common stock, $0.001 par value; 100,000 shares authorized:
   36,017 shares in 1999 and 34,923 shares in 1998 issued and
   outstanding                                                           36             35
   Additional paid-in capital                                       310,614        296,370
   Deferred compensation                                               (543)          (957)
   Notes receivable from officers                                       (46)           (87)
   Other comprehensive income (loss)                                   (734)            29
   Accumulated deficit                                              (85,952)       (89,028)
                                                                  ---------      ---------
Total stockholders' equity                                          223,375        206,362
                                                                  ---------      ---------

Total liabilities and stockholders' equity                        $ 302,741      $ 257,954
                                                                  =========      =========
</TABLE>


See notes to condensed consolidated financial statements.


<PAGE>   4

<TABLE>
<CAPTION>

                                       MILLENNIUM PHARMACEUTICALS, INC.
                                CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS
                                                  (UNAUDITED)


                                             THREE MONTHS ENDED               SIX MONTHS ENDED
                                                 JUNE 30,                         JUNE 30,
(IN THOUSANDS, EXCEPT PER SHARE AMOUNTS)    1999            1998            1999           1998
                                          --------        --------        --------       ---------
<S>                                       <C>             <C>             <C>             <C>
Revenue under strategic alliances         $ 47,273        $ 28,236        $ 88,265        $ 49,279

Costs and expenses:
   Research and development                 39,484          28,036          74,917          50,465
   General and administrative                8,502           5,927          15,628          11,838
   Amortization of intangible asset            675             676           1,351           1,351
                                          --------        --------        --------        --------
                                            48,661          34,639          91,896          63,654
                                          --------        --------        --------        --------
Loss from operations                        (1,388)         (6,403)         (3,631)        (14,375)

Interest income                              3,133           1,339           5,892           2,786
Interest expense                              (775)           (479)         (1,472)         (1,124)
Minority interest                               34           3,342           2,287           6,086
                                          --------        --------        --------        --------

Net income (loss)                         $  1,004        $ (2,201)       $  3,076        $ (6,627)
                                          ========        ========        ========        ========

Basic net income (loss) per share         $   0.03        $  (0.07)       $   0.09        $  (0.23)
                                          ========        ========        ========        ========
Diluted net income (loss) per share       $   0.03        $  (0.07)       $   0.08        $  (0.23)
                                          ========        ========        ========        ========

SHARES USED IN CALCULATING:
Basic net income (loss) per share           35,819          29,501          35,570          29,397
                                          ========        ========        ========        ========
Diluted net income (loss) per share         38,491          29,501          38,188          29,397
                                          ========        ========        ========        ========
</TABLE>


See notes to condensed consolidated financial statements.

<PAGE>   5


<TABLE>
<CAPTION>

                        MILLENNIUM PHARMACEUTICALS, INC.
                 CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS
                                   (UNAUDITED)

                                                           SIX MONTHS ENDED JUNE 30,
(IN THOUSANDS)                                               1999            1998
                                                          ---------        --------
<S>                                                       <C>              <C>
CASH PROVIDED BY (USED IN) OPERATIONS                     $  15,600        $(17,906)
                                                          ---------        --------

INVESTING ACTIVITIES
Purchase of property and equipment                          (14,931)         (3,004)
Sale of marketable securities                                31,025          35,785
Purchase of marketable securities                          (154,573)        (48,936)
                                                          ---------        --------
Net cash used in investing activities                      (138,479)        (16,155)
                                                          ---------        --------

FINANCING ACTIVITIES
Proceeds from sale of subsidiary stock                       15,000              --
Net proceeds from stock option exercises                     14,247           2,134
Repurchase of Common Stock                                       (1)            (15)
Payments of capital lease obligations                        (4,204)         (3,216)
                                                          ---------        --------
Net cash provided by (used in) financing activities          25,042          (1,097)
                                                          ---------        --------

Decrease in cash and cash equivalents                       (97,837)        (35,158)
Cash and cash equivalents at beginning of period            138,284          69,236
                                                          ---------        --------
Cash and cash equivalents at end of period                $  40,447        $ 34,078
                                                          =========        ========

NONCASH INVESTING AND FINANCING ACTIVITIES:
Equipment acquired under capital leases                   $   4,700        $  5,395
                                                          =========        ========
</TABLE>


See notes to condensed consolidated financial statements.



<PAGE>   6


                        MILLENNIUM PHARMACEUTICALS, INC.
              NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS
                                  JUNE 30, 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 and six month periods ended June
30, 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 and Exchange Commission on March 24, 1999.

     In June 1998, the Financial Accounting Standards Board issued Statement of
Financial Accounting Standards No. 133, "Accounting for Derivative Instruments
and Hedging Activities", which is effective for fiscal years beginning after
June 15, 2000. 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.

     Comprehensive income (loss) is composed of net income (loss) and other
comprehensive income (loss). Other comprehensive income (loss) is composed of
changes in equity that are excluded from net income (loss) resulting from
unrealized holding gains and losses on available-for-sale marketable securities.
Comprehensive income (loss) for the three months ended June 30, 1999 and 1998
was $0.4 million and $ (2.2) million, respectively. Comprehensive income (loss)
for the six months ended June 30, 1999 and 1998 was $2.3 million and $ (6.6)
million, respectively.

     Net income per share for the three and six months ended June 30, 1999 is
computed using the weighted-average number of common shares and
dilutive-equivalent shares from stock options and warrants using the treasury
stock method. Net loss per share for the three and six months ended June 30,
1998 is computed using the weighted-average number of common shares outstanding.
For the three and six months ended June 30, 1999 the difference between basic
and diluted shares used in the computation of earnings per share is 2.7 million
and 2.6 million weighted-average common equivalent shares resulting from
outstanding common stock options and warrants, respectively.



                                       6

<PAGE>   7


2-   STRATEGIC ALLIANCE

     On February 22, 1999, the Company announced the formation of a strategic
alliance in the diagnostics 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
focuses 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 any related product sales.

     On March 31, 1999, Becton Dickinson made an equity investment in MPMx of
$15.0 million, representing approximately an 11% voting interest in MPMx, and
paid a $3.0 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,
provided the alliance continues for the full 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.





                                       7
<PAGE>   8



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. A number of 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 has developed 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, Millennium BioTherapeutics,
Inc, ("MBio") and Millennium Predictive Medicine, Inc. ("MPMx"), where
appropriate in the context.

     To date, all of our revenue has resulted from payments from strategic
partners and United States Government research grants. We have not received any
revenue from the sale of products.

     These strategic alliance agreements have provided Millennium with various
combinations of equity investments, up-front and follow-on fees and research
funding. These alliances may also provide certain additional payments upon the
attainment of research and regulatory milestones as well as royalty and/or
profit sharing payments based on sales of any products resulting from the
collaborations. However, there can be no assurance that any of our strategic
alliance agreements will continue for their full term or be renewed on terms
favorable to the Company if at all or that any of the discoveries will result in
marketed products.

     During 1999, we expect to continue to pursue additional alliances, and will
consider joint development and acquisition opportunities that may provide
Millennium with access to products on the market or in later stages of
commercial development than those represented within our current programs. We
expect that Millennium will incur increasing expenses and may incur increasing
operating losses for at least the next several years, primarily due to expansion
of facilities and research and development programs as a result of acquisitions
and as a result of



                                       8

<PAGE>   9


efforts to advance acquired products or our own development programs to
commercialization. Our revenues under existing and new strategic alliances may
fluctuate from period to period or year to year; these fluctuations, as well as
fluctuations in spending, may result in periods of profitability and periods of
losses. Therefore, Millennium's results of operations for any period may not be
indicative of future results of operations.

RESULTS OF OPERATIONS

     QUARTERS ENDED JUNE 30, 1999 AND JUNE 30, 1998

     For the quarter ended June 30, 1999 (the "1999 Quarterly Period"), the
Company reported net income of $1.0 million or $0.03 per basic and diluted share
as compared to a net loss of $2.2 million or $0.07 per basic and diluted share
for the quarter ended June 30, 1998 ("the 1998 Quarterly Period").

     Revenue under strategic alliances increased to $47.3 million for the 1999
Quarterly Period from $28.2 million for the 1998 Quarterly Period. The increase
in revenue is primarily due to revenue from an alliance with Bayer AG that was
not in place in the 1998 Quarterly Period. We expect revenues to increase in the
near term, however, revenues may fluctuate from period to period and there can
be no assurance that strategic alliance agreements will continue for their
initial term or beyond.

     Research and development expenses increased to $39.5 million for the 1999
Quarterly Period from $28.0 million for the 1998 Quarterly Period. The increase
was primarily attributable to increased personnel and facilities expenses,
increased purchases of laboratory supplies, 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 and additional strategic alliances and
development efforts for potential new product candidates.

     General and administrative expenses increased to $8.5 million for the 1999
Quarterly Period from $5.9 million for the 1998 Quarterly Period. The increase
was attributable primarily to increased facilities and 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 we add capabilities to support the further
advancement of new product candidates.

     Interest income increased to $3.1 million for the 1999 Quarterly Period
from $1.3 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 $0.8 million for the 1999
Quarterly Period from $0.5 million for the 1998 Quarterly Period due to
increased capital lease obligations.


                                       9

<PAGE>   10


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

SIX MONTHS ENDED JUNE 30, 1999 AND JUNE 30, 1998

     For the six months ended June 30, 1999 (the "1999 Six Month Period"), the
Company reported net income of $3.1 million or $0.09 per basic share and $0.08
per diluted share as compared to a net loss of $6.6 million or $0.23 per basic
and diluted share for the six months ended June 30, 1998 (the "1998 Six Month
Period").

     Revenue under strategic alliances increased to $88.3 million for the 1999
Six Month Period from $49.3 million for the 1998 Six Month Period. The increase
is primarily due to revenue from an alliance with Bayer AG that was not in place
in the 1998 Six Month Period. We expect revenues to increase in the near term,
however, revenues may fluctuate from period to period and there can be no
assurance that strategic alliance agreements will continue for their initial
term or beyond.

     Research and development expenses increased to $74.9 million for the 1999
Six Month Period from $50.5 million for the 1998 Six Month Period. The increase
was attributable primarily to increased personnel expenses as the Company hired
additional research and development personnel, increased purchases of laboratory
supplies, and increased equipment depreciation and facilities expenses in
connection with the expansion of the Company's research efforts. 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 development efforts for potential new product
candidates.

     General and administrative expenses increased to $15.6 million for the 1999
Six Month Period from $11.8 million for the 1998 Six Month Period. The increase
was attributable primarily to increased personnel expenses as the Company hired
additional management, business development, and administrative personnel, and
to increased facilities costs and professional fees in connection with the
further expansion of the Company's operations. We expect that general and
administrative expenses will continue to increase as we add capabilities to
support the further advancement of new product candidates.

     Interest income increased to $5.9 million for the 1999 Six Month Period
from $2.8 million for the 1998 Six Month Period. The increase resulted from an
increase in the Company's average balance of cash, cash equivalents and
marketable securities. Interest expense increased to $1.5 million for the 1999
Six Month Period from $1.1 million for the 1998 Six Month Period due to
increased capital lease obligations.


                                       10

<PAGE>   11


     Minority interest represents the minority shareholder interest of Lilly in
the net income or loss for the 1999 and 1998 Six Month Periods of the Company's
majority-owned subsidiary, MBio, as well as the minority shareholder interest of
Becton Dickinson in the net income or loss for the 1999 Six Month Period of the
Company's majority-owned subsidiary, MPMx.

LIQUIDITY AND CAPITAL RESOURCES

     As of June 30, 1999, the Company had approximately $215.9 million in cash,
cash equivalents and marketable securities. This excludes $11.2 million of
interest-bearing marketable securities classified as restricted cash and other
assets on the balance sheet which serve as security deposits for certain of the
Company's facilities leases.

     During the six months ended June 30, 1999, $15.6 million of cash was
provided by operations. Other inflows of cash were generated from the sale of
marketable securities of $31.0 million, the sale of MPMx stock of $15.0 million
to Becton Dickinson and proceeds from exercise of stock options of $14.2
million. Cash outflows included the purchase of $14.9 million of property and
equipment, $154.6 million of investments in marketable securities and $4.2
million to pay capital lease obligations.

     On February 22, 1999, the Company announced the formation of a strategic
alliance in the diagnostics field between its wholly-owned subsidiary, MPMx, and
Becton Dickinson. The five-year genomics-based research collaboration focuses on
several areas of oncology. On March 31, 1999, Becton Dickinson made an equity
investment in MPMx of $15.0 million, representing approximately an 11% voting
interest in MPMx, and paid a $3.0 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.

     Millennium has financed its operations since inception primarily through
strategic alliances, equity security offerings, issuance of debt, and capital
leases.

     We believe that existing cash and investment securities, and anticipated
cash flow from our current strategic alliances will be sufficient to support our
existing operations for the near term. Millennium's actual future cash
requirements, however, will depend on many factors, including progress of our
disease research programs, the number and breadth of these programs, achievement
of milestones under strategic alliance arrangements, acquisitions, our ability
to establish and maintain additional strategic alliance and licensing
arrangements, and the progress of the development efforts of our strategic
partners. We expect that Millennium will require significant additional
financing in the future, which we may seek to raise through public or private
equity offerings, debt financings, additional strategic alliances or other
financing vehicles. However, we can make no assurance that additional financing,
strategic alliances or licensing arrangements will be available when needed or
that, if available, such financing will be



                                       11

<PAGE>   12


obtained on terms favorable to the Company or its stockholders. The Company's
forecast of the period of time through which its financial resources will be
adequate to support its operations is forward-looking information, and, as such,
actual results may vary.


NEW ACCOUNTING PRONOUNCEMENT

     In June 1998, the Financial Accounting Standards Board issued Statement of
Financial Accounting Standards No. 133, "Accounting for Derivative Instruments
and Hedging Activities", which is effective for fiscal years beginning after
June 15, 2000. The Company believes the adoption of this new accounting standard
will not have a significant effect on its financial statements as the Company's
investment policies prohibit the use of derivatives.


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 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 an inventory and assessment of our informatics applications. 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 have identified critical
systems and equipment on which to focus our inquiries, remediation efforts, and
testing.


                                       12

<PAGE>   13


     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 for identified critical systems and equipment. 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 the first
quarter of 1999. We obtained and reviewed 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 that 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.

     We have begun developing contingency plans for critical aspects of our
systems and operations to address Year 2000 problems that may arise despite our
Year 2000 compliance efforts.

     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.



                                       13
<PAGE>   14


ITEM 3. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

     The Company maintains an investment portfolio in accordance with its
Investment Policy. The primary objectives of the Company's Investment Policy are
to preserve principal, maintain proper liquidity to meet operating needs and
maximize yields. The Company's Investment Policy specifies credit quality
standards for the Company's investments and limits the amount of credit exposure
to any single issue, issuer or type of investment.

     The Company does not believe that there is any material market risk
exposure with respect to derivative or other financial instruments which would
require disclosure under this item.

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

     The Company's 1999 Annual Meeting of Stockholders was held on June 2, 1999
(the "Annual Meeting"). The following is a summary of each matter voted upon at
the Annual Meeting and the number of votes cast for, against or withheld, and
broker non-votes and abstentions, as to each such matter:

     1. Election of three Class III directors, each for a term of three years.


     Mark J. Levin:             For:  31,210,928 Withheld:  329,395
     Joshua Boger, Ph.D.:       For:  31,210,928 Withheld:  329,395
     A. Grant Heidrich III:     For:  31,194,388 Withheld:  345,935

     2. Approval of an amendment to the Company's 1996 Equity Incentive Plan
     increasing the number of shares of Common Stock reserved for issuance from
     4,100,000 to 5,600,000.

     For: 16,735,659  Against: 10,071,581  Abstain: 30,222  Non-votes: 4,702,861

     3. Approval of an amendment to the Company's 1997 Equity Incentive Plan
     increasing the number of shares of Common Stock reserved for issuance from
     2,000,000 to 4,000,000.

     For:  17,659,014 Against:  9,143,931  Abstain: 34,517  Non-votes: 4,702,861

     4. Approval of an amendment to the Company's 1996 Employee Stock Purchase
     Plan increasing the number of shares of Common Stock reserved for issuance
     from 350,000 to 650,000.

     For:  26,677,003  Against: 127,880  Abstain:  32,579 Non-votes: 4,702,861



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<PAGE>   15


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

          None.




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<PAGE>   16



                                   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:  July 30, 1999                   By: /s/ Kevin P. Starr
                                           ------------------------------------
                                           Kevin P. Starr
                                           Chief Financial Officer
                                           (Principal Financial and Accounting
                                           Officer)




                                       16


<PAGE>   17


                                  EXHIBIT INDEX

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

Exhibit
  No.          Description
-------        -----------

+10.1          Agreement dated February 21, 1999 by and between Millennium
               Predictive Medicine, Inc. and Becton, Dickinson and Company

 10.2          Amended and Restated Rights Exchange Agreement dated February 1,
               1999 between Millennium Pharmaceuticals, Inc. and Millennium
               Predictive Medicine, Inc.

 10.3          Technology Transfer and License Agreement dated February 1, 1999
               between Millennium Pharmaceuticals, Inc. and Millennium
               Predictive Medicine, Inc.

 27.1          Financial Data Schedule for the quarter ended June 30, 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).



+ Confidential treatment requested with respect to certain portions




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