<Page>

                                                                   EXHIBIT 10.29

                        MILLENNIUM PHARMACEUTICALS, INC.
                                75 SIDNEY STREET
                               CAMBRIDGE, MA 02139

                                                               December 24, 2002

Charles J. Homcy
c/o Millennium Pharmaceuticals, Inc.
75 Sidney Street
Cambridge, MA 02139

Dear Mr. Homcy:

     This letter memorializes certain verbal agreements between you and
Millennium Pharmaceuticals, Inc. ("Millennium") that we made upon the merger
(the "Merger") of Millennium with COR Therapeutics, Inc. ("COR") on February 12,
2002.

     1.   As an "eligible employee" under the COR Key Employee Severance Plan
(the "Plan"), you would be entitled to certain benefits upon the termination of
your employment for certain specified reasons following the Merger. We have
agreed to provide the benefits described in Section 4(a) (Base Salary) based on
your salary at the time of the Merger of $381,600, 4(b) (Bonus) based on your
bonus target at the time of the Merger of 50% and 4(c) (Health Benefits) of the
Plan if your employment with Millennium terminates for any reason on or prior to
February 12, 2004 and the Plan does not otherwise provide you benefits for such
a termination. Millennium will make salary continuation payments in regular
installments on the normal payroll dates of Millennium, or over a shorter period
as determined by Millennium. Millennium will pay you the pro rata bonus benefit
based on the actual funding for the year as determined by the Board of
Directors, with such payment being made at the same time as payments for other
executives of the Company. Any such amounts that you receive will be subject to
all required tax withholding.

     2.   If your employment with Millennium terminates for any reason on or
prior to February 12, 2004, any outstanding options to purchase shares of the
common stock of Millennium ("Options") held by you on February 12, 2002
(immediately after the Merger) will immediately vest and become exercisable in
full as of the date of such termination. All such Options will otherwise remain
subject to the terms and conditions set forth in the applicable stock option
plans and stock option agreements.

     3.   If any payment or benefit you would receive pursuant to this
agreement, when combined with any other payment or benefit you receive pursuant
to the termination of your employment with Millennium ("Payment") would (i)
constitute a "parachute payment" within the meaning of Section 280G of the
Internal Revenue Code of 1986, as amended (the "Code"), and (ii) but for this
sentence, be subject to the excise tax imposed by Section 4999 of the Code (the
"Excise Tax"), then such Payment will be either (x) the full amount of Payment
or (y) such

<Page>

lesser amount (with cash payments being reduced before stock option
compensation) as would result in no portion of the Payment being subject to the
Excise Tax, whichever of the foregoing amounts, taking into account the
applicable federal, state and local employment taxes, income taxes, and the
Excise Tax results in your receipt, on an after-tax basis, of the greater amount
of the Payment notwithstanding that all or some portion of the Payment may be
subject to the Excise Tax.

     4.   The Plan, including the requirement for a release under Section 4(e),
remains in full force and effect, except as augmented in this letter agreement.

     5.   This agreement may be amended or modified only by a written instrument
executed by you and Millennium. This agreement will be interpreted and enforced
in accordance with the laws of the Commonwealth of Massachusetts.

     Please acknowledge your agreement by countersigning this letter below.

                                Sincerely,

                                MILLENNIUM PHARMACEUTICALS, INC.


                                By:/s/ JOHN B. DOUGLAS III
                                       -------------------
                                Name:  John B. Douglas III
                                Title: Senior Vice President and General Counsel


AGREED TO:


/s/ CHARLES J. HOMCY
    ----------------
Charles J. Homcy