MILLENNIUM PHARMACEUTICALS INC
424B3, 2000-09-11
PHARMACEUTICAL PREPARATIONS
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<PAGE>

                                              Filed Pursuant to Rule 424(b)(3)
                                              Registration No. 333-31344


PROSPECTUS SUPPLEMENT
(TO PROSPECTUS DATED APRIL 27, 2000)

                        MILLENNIUM PHARMACEUTICALS, INC.

       $400,000,000 Principal Amount 5.50% Convertible Subordinated Notes
                              Due January 15, 2007

     4,753,920 Shares of Common Stock issuable upon conversion of the Notes

      211,554 Shares of Common Stock issuable upon exercise of outstanding
                       warrants to purchase common stock

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

         This prospectus supplement relates to resales by selling holders of:

         -    our 5.50% Convertible Subordinated Notes due January 15, 2007;

         -    our common stock into which the notes are convertible; and

         -    our common stock issuable upon exercise of warrants to purchase
              our common stock held by GATX Capital Corporation and MM Ventures

         This prospectus supplement should be read in conjunction with the
prospectus dated April 27, 2000, which is to be delivered with this prospectus
supplement.

         SEE "RISK FACTORS" BEGINNING ON PAGE 6 OF THE PROSPECTUS TO READ ABOUT
FACTORS YOU SHOULD CONSIDER BEFORE BUYING THE NOTES OR OUR COMMON STOCK.

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

         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.

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

         The information in the table appearing in the prospectus under the
heading "Selling Holders" is superseded in part by the information appearing in
the following table:

<TABLE>
<CAPTION>
                                                                           Number of
                                                            Percentage     Shares of
                        Notes                    Notes        of the         Common     Number of      Number of     Percentage
                     Beneficially             Beneficially    Notes          Stock      Shares of      Shares of    of Shares of
                        Owned       Notes        Owned      Beneficially  Beneficially   Common      Common Stock   Common Stock
                       Prior to     Offered      After        Owned          Owned       Stock       Beneficially   Beneficially
   Selling             Offering     Hereby    Offering (1)   After the     Prior to      Offered     Owned After    Owned After
Securityholder       (in $1,000)  (in $1,000) (in $1,000)    Offering      Offering      Hereby      Offering(1)    Offering(1)
<S>                  <C>          <C>         <C>           <C>           <C>           <C>          <C>            <C>

Amoco Corp.               656         656            0            0          7,796       7,796              0              0
Master Trust

Arkansas                2,132       2,132            0            0         25,338      25,338              0              0
Teachers
Retirement
System

<PAGE>


<CAPTION>
                                                                           Number of
                                                            Percentage     Shares of
                        Notes                    Notes        of the         Common     Number of      Number of     Percentage
                     Beneficially             Beneficially    Notes          Stock      Shares of      Shares of    of Shares of
                        Owned       Notes        Owned      Beneficially  Beneficially   Common      Common Stock   Common Stock
                       Prior to     Offered      After        Owned          Owned       Stock       Beneficially   Beneficially
   Selling             Offering     Hereby    Offering (1)   After the     Prior to      Offered     Owned After    Owned After
Securityholder       (in $1,000)  (in $1,000) (in $1,000)    Offering      Offering      Hereby      Offering(1)    Offering(1)
<S>                  <C>          <C>         <C>           <C>           <C>           <C>          <C>            <C>

Associated                450         450            0            0          5,348       5,348              0              0
Electric & Gas
Insurance
Services Limited

Baptist Health            103         103            0            0          1,224       1,224              0              0
of South Florida

Boston Museum              83          83            0            0            986         986              0              0
of Fine Arts

Champion                  393         393            0            0          4,670       4,670              0              0
International
Corp.

City University            87          87            0            0          1,033       1,033              0              0
of New  York

Credit Suisse           2,818       2,818            0            0         33,491      33,491              0              0
First Boston
Corporation

David Lipscomb            105         105            0            0          1,247       1,247              0              0
University
General
Endowment

Deephaven              10,886      10,886            0            0        129,377     129,377              0              0
Domestic
Convertible
Trading Ltd

Donaldson,                575         575            0            0          6,833       6,833              0              0
Lufkin &
Jenrette
Securities Corp.

Engineers Joint           289         289            0            0          3,434       3,434              0              0
Pension Fund

EQAT Alliance           2,955       2,955            0            0         35,119      35,119              0              0
Growth & Income

Equitable Life          1,925       1,925            0            0         22,878      22,878              0              0
Assurance
Separate
Account -
Convertible


                                       2
<PAGE>


<CAPTION>
                                                                           Number of
                                                            Percentage     Shares of
                        Notes                    Notes        of the         Common     Number of      Number of     Percentage
                     Beneficially             Beneficially    Notes          Stock      Shares of      Shares of    of Shares of
                        Owned       Notes        Owned      Beneficially  Beneficially   Common      Common Stock   Common Stock
                       Prior to     Offered      After        Owned          Owned       Stock       Beneficially   Beneficially
   Selling             Offering     Hereby    Offering (1)   After the     Prior to      Offered     Owned After    Owned After
Securityholder       (in $1,000)  (in $1,000) (in $1,000)    Offering      Offering      Hereby      Offering(1)    Offering(1)
<S>                  <C>          <C>         <C>           <C>           <C>           <C>          <C>            <C>

EQAT Alliance           1,605       1,605            0            0         19,075      19,075              0              0
Growth Investors

Fidelity                8,250       8,250            0            0         98,049      98,049
Financial
Trust:
Fidelity
Convertible &
Securities Fund

Forest                    109         109            0            0          1,295       1,295              0              0
Alternative
Strategies Fund
II LP A5M

Forest Fulcrum            900         900            0            0         10,696      10,696              0              0
Fund LP

Forest Global           6,625       6,625            0            0         78,736      78,736              0              0
Convertible
Fund A-5

Goldman Sachs          16,276      16,276            0            0        193,437     193,437              0              0
and Company

Grady Hospital            136         136            0            0          1,616       1,616              0              0

Helix                   1,065       1,065            0            0         12,657      12,657              0              0
Convertible
Opportunities
Fund Ltd.

Helix                   3,095       3,095            0            0         36,783      36,783              0              0
Convertible
Opportunities,
L.P.

HBK Master Fund         2,500       2,500            0            0         29,712      29,712              0              0
L.P.

Jeffries & Co.            656         656            0            0          7,796       7,796              0              0
Inc.

JAS Securities          1,500       1,500            0            0         17,827      17,827              0              0

J.P. Morgan             7,054       7,054            0            0         83,835      83,835              0              0
Securities Inc.

KBC Financial           2,000       2,000            0            0         23,769      23,769              0              0
Products



                                       3
<PAGE>


<CAPTION>
                                                                           Number of
                                                            Percentage     Shares of
                        Notes                    Notes        of the         Common     Number of      Number of     Percentage
                     Beneficially             Beneficially    Notes          Stock      Shares of      Shares of    of Shares of
                        Owned       Notes        Owned      Beneficially  Beneficially   Common      Common Stock   Common Stock
                       Prior to     Offered      After        Owned          Owned       Stock       Beneficially   Beneficially
   Selling             Offering     Hereby    Offering (1)   After the     Prior to      Offered     Owned After    Owned After
Securityholder       (in $1,000)  (in $1,000) (in $1,000)    Offering      Offering      Hereby      Offering(1)    Offering(1)
<S>                  <C>          <C>         <C>           <C>           <C>           <C>          <C>            <C>

Key Asset                 350         350            0            0          4,159       4,159              0              0
Management,
Inc., as Agent
for the Victory
Convertible
Securities Fund

Lehman                    148         148            0            0          1,758       1,758              0              0
Brothers, Inc.

Local                      56          56            0            0            665         665              0              0
Initiatives
Support
Corporation

Lord Abbett             7,600       7,600            0            0         90,324      90,324              0              0
Bond Debenture
Fund

Lyxor Master            1,000       1,000            0            0         11,884      11,884              0              0
Fund c/o Forest
Investment
Management LLC

Maryland State          3,397       3,397            0            0         40,372      40,372              0              0
Retirement
System

New Orleans               139         139            0            0          1,651       1,651              0              0
Firefighters

Nicholas-Applegate        738         738            0            0          8,770       8,770              0              0
Convertible Fund

Occidental                240         240            0            0          2,852       2,852              0              0
Petroleum

Physicians Life           226         226            0            0          2,685       2,685              0              0

Q Opportunity           3,500       3,500            0            0         41,596      41,596              0              0
Fund Ltd.

Robertson               8,000       8,000            0            0         95,078      95,078              0              0
Stephens



                                       4
<PAGE>


<CAPTION>
                                                                           Number of
                                                            Percentage     Shares of
                        Notes                    Notes        of the         Common     Number of      Number of     Percentage
                     Beneficially             Beneficially    Notes          Stock      Shares of      Shares of    of Shares of
                        Owned       Notes        Owned      Beneficially  Beneficially   Common      Common Stock   Common Stock
                       Prior to     Offered      After        Owned          Owned       Stock       Beneficially   Beneficially
   Selling             Offering     Hereby    Offering (1)   After the     Prior to      Offered     Owned After    Owned After
Securityholder       (in $1,000)  (in $1,000) (in $1,000)    Offering      Offering      Hereby      Offering(1)    Offering(1)
<S>                  <C>          <C>         <C>           <C>           <C>           <C>          <C>            <C>

Pilgrim                 2,765       2,765            0            0         32,861      32,861              0              0
Convertible Fund

S G Cowen               7,000       7,000            0            0         83,193      83,193              0              0
Securities Corp.

Sagamore Hill           6,250       6,250            0            0         74,280      74,280              0              0
Hub Fund Ltd.

San Diego City            580         580            0            0          6,893       6,893              0              0
Retirement

San Diego               1,408       1,408            0            0         16,733      16,733              0              0
County
Convertible

Shell Pension             376         376            0            0          4,468       4,468              0              0
Trust

The Common Fund           560         560            0            0          6,655       6,655              0              0
FAO Absolute
Return Fund

The Frist                 285         285            0            0          3,387       3,387              0              0
Foundation

Tribeca                29,000      24,000            0            0        344,659     285,235              0              0
Investments LLC

Wake Forest               692         692            0            0          8,224       8,224              0              0
University

Writers                   179         179            0            0          2,127       2,127              0              0
Guild-Industry
Health Fund
</TABLE>



                                       5
<PAGE>


         (1) We do not know if, when or in what amounts a selling securityholder
may offer securities for sale and we do not know that the selling
securityholders will sell any or all of the securities offered hereby. Because
the selling securityholders may offer all or some of the securities pursuant to
this prospectus, and because there are currently no other agreements,
arrangements or understandings with respect to the sale of any of the securities
that will be held by the selling securityholders, no estimate can be given as to
the amount of the securities that will be held by the selling securityholders
after completion of the offering made by this prospectus. However, for purposes
of this table, we have assumed that, after completion of the offering, no
securities will be held by the selling securityholders.

         The date of this prospectus supplement is September 11, 2000.



                                       6



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