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                                                                    Exhibit 10.1

                            COMBINATORX, INCORPORATED

                             2000 STOCK OPTION PLAN


     1.   PURPOSE.

     The purpose of this plan (the "Plan") is to secure for CombinatoRx,
Incorporated (the "Corporation") and its shareholders the benefits arising from
capital stock ownership by employees, officers and directors of, and consultants
or advisors to, the Corporation and its Parent and subsidiary corporations who
are expected to contribute to the Corporation's future growth and success.
Except where the context otherwise requires, the term "Corporation" shall
include the parent and all present and future subsidiaries of the Corporation as
defined in Sections 424(e) and 424(f) of the Internal Revenue Code of 1986, as
amended or replaced from time to time (the "Code"). Those provisions of the Plan
which make express reference to Section 422 shall apply only to Incentive Stock
Options (as that term is defined in the Plan).

     2.   TYPE OF OPTIONS AND ADMINISTRATION.

     (a)  TYPES OF OPTIONS. Options granted pursuant to the Plan shall be
authorized by action of the Board of Directors of the Corporation (or a
Committee designated by the Board of Directors) and may be either incentive
stock options ("Incentive Stock Options") meeting the requirements of Section
422 of the Code or non-statutory options which are not intended to meet the
requirements of Section 422 of the Code.

     (b)  ADMINISTRATION. The Plan will be administered by the Board of
Directors of the Corporation, whose construction and interpretation of the terms
and provisions of the Plan shall be final and conclusive. The Board of Directors
may in its sole discretion grant options to purchase shares of the Corporation's
$0.001 common stock ("Common Stock") and issue shares upon exercise of such
options as provided in the Plan. The Board shall have authority, subject to the
express provisions of the Plan, to construe the respective option agreements and
the Plan, to prescribe, amend and rescind rules and regulations relating to the
Plan, to determine the terms and provisions of the respective option agreements,
which need not be identical, and to make all other determinations in the
judgment of the Board of Directors necessary or desirable for the administration
of the Plan. The Board of Directors may correct any defect or supply any
omission or reconcile any inconsistency in the Plan or in any option agreement
in the manner and to the extent it shall deem expedient to carry the Plan into
effect and it shall be the sole and final judge of such expediency. No director
or person acting pursuant to authority delegated by the Board of Directors shall
be liable for any action or determination under the Plan made in good faith. To
the extent permitted by applicable law, the Board of Directors may delegate any
or all of its powers under the Plan to one or more committees or subcommittees
of the Board of Directors (a "Committee"). If and when the Common Stock is
registered under the Securities Exchange Act of 1934 (the "Exchange Act") the
Board of Directors shall appoint one such Committee of not less than two
members, each member of which shall be an "outside director" within the meaning
of Section 162(m) of the Code and a "non-employee director" as defined in

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Rule 16b-3 promulgated under the Exchange Act). All references in the Plan to
the Board of Directors shall mean the Board of Directors or a Committee of the
Board of Directors to the extent that the Board's powers or authority under the
Plan have been delegated to such Committee.

     3.   ELIGIBILITY.

     Options may be granted to persons who are, at the time of grant, employees,
officers or directors of, or consultants or advisors to, the Corporation, its
parent, or any subsidiary; PROVIDED, that the class of employees to whom
Incentive Stock Options may be granted shall be limited to all employees of the
Corporation, its parent, or any subsidiary. A person who has been granted an
option may, if he or she is otherwise eligible, be granted additional options if
the Board of Directors shall so determine.

     4.   STOCK SUBJECT TO PLAN.

     Subject to adjustment as provided in Section 15 below, the maximum number
of shares of Common Stock of the Corporation which may be issued and sold under
the Plan is Ten Thousand (10,000) shares. If an option granted under the Plan
shall expire or terminate for any reason without having been exercised in full,
the unpurchased shares subject to such option shall again be available for
subsequent option grants under the Plan. If shares issued upon exercise of an
option under the Plan are tendered to the Corporation in payment of the exercise
price of an option granted under the Plan, such tendered shares shall again be
available for subsequent option grants under the Plan; provided, that in no
event shall such shares be made available pursuant to exercise of Incentive
Stock Options.

     5.   FORMS OF OPTION AGREEMENTS.

     As a condition to the grant of an option under the Plan, each recipient of
an option shall execute an option agreement in such form not inconsistent with
the Plan as may be approved by the Board of Directors. Such option agreements
may differ among recipients.

     6.   PURCHASE PRICE.

     (a)  GENERAL. The purchase price per share of stock deliverable upon the
exercise of an option shall be determined by the Board of Directors, PROVIDED,
HOWEVER, that in the case of an Incentive Stock Option, the exercise price shall
not be less than 100% of the fair market value of such stock, as determined by
the Board of Directors, at the time of grant of such option, or less than 110%
of such fair market value in the case of options described in Section 11(b).

     (b)  PAYMENT OF PURCHASE PRICE. Options granted under the Plan may provide
for the payment of the exercise price by delivery of cash or a check to the
order of the Corporation in an amount equal to the exercise price of such
options, or, to the extent provided in the applicable option agreement, (i) by
delivery to the Corporation of shares of Common Stock of the Corporation already
owned by the optionee having a fair market value equal in amount to the exercise
price of the options being exercised, (ii) by any other means (including,
without

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limitation, by delivery of a promissory note of the optionee payable on such
terms as are specified by the Board of Directors) which the Board of Directors
determines are consistent with the purpose of the Plan and with applicable laws
and regulations (including, without limitation, the provisions of Rule 16b-3 and
Regulation T promulgated by the Federal Reserve Board) or (iii) by any
combination of such methods of payment. The fair market value of any shares of
the Corporation's Common Stock or other non-cash consideration which may be
delivered upon exercise of an option shall be determined by the Board of
Directors.

     7.   OPTION PERIOD.

     Each option and all rights thereunder shall expire on such date as shall be
set forth in the applicable option agreement, except that, in the case of an
Incentive Stock Option, such date shall not be later than ten years after the
date on which the option is granted and, in all cases, options shall be subject
to earlier termination as provided in the Plan.

     8.   EXERCISE OF OPTIONS.

     Each option granted under the Plan shall be exercisable either in full or
in installments at such time or times and during such period as shall be set
forth in the agreement evidencing such option, subject to the provisions of the
Plan.

     9.   NONTRANSFERABILITY OF OPTIONS.

     Except as the Board of Directors may otherwise determine or provide in an
option, options shall not be assignable or transferable by the person to whom
they are granted, either voluntarily or by operation of law, except by will or
the laws of descent and distribution, and, during the life of the optionee,
shall be exercisable only by the optionee; provided, however, that non-statutory
options may be transferred pursuant to a qualified domestic relations order (as
defined in Code Section 414(p)).

     10.  EFFECT OF TERMINATION OF EMPLOYMENT OR OTHER RELATIONSHIP.

     Subject to the provisions of the Plan, the Board of Directors shall
determine the period of time during which an optionee may exercise an option
following (i) the termination of the optionee's employment or other relationship
with the Corporation, its parent, or any subsidiary, or (ii) the death or
disability of the optionee. Such periods shall be set forth in the agreement
evidencing such option. Employment shall not be deemed to be terminated because
an optionee is transferred from one of the Corporation, its parent, or any
subsidiary to another one of the Corporation, its parent, or any subsidiary.

     11.  INCENTIVE STOCK OPTIONS.

     Options granted under the Plan which are intended to be Incentive Stock
Options shall be subject to the following additional terms and conditions:

     (a)  EXPRESS DESIGNATION. All Incentive Stock Options granted under the
Plan shall, at

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the time of grant, be specifically designated as such in the option agreement
covering such Incentive Stock Options.

     (b)  10% SHAREHOLDER. If any employee to whom an Incentive Stock Option is
to be granted under the Plan is, at the time of the grant of such option, the
owner of stock possessing more than 10% of the total combined voting power of
all classes of stock of the Corporation (after taking into account the
attribution of stock ownership rules of Section 424(d) of the Code), then the
following special provisions shall be applicable to the Incentive Stock Option
granted to such individual:

          (i)     the purchase price per share of the Common Stock subject to
     such Incentive Stock Option shall not be less than 110% of the fair market
     value of one share of Common Stock at the time of grant; and

          (ii)    the option exercise period shall not exceed five years from
     the date of grant.

     (c)  DOLLAR LIMITATION. For so long as the Code shall so provide, options
granted to any employee under the Plan (and any other incentive stock option
plans of the Corporation) which are intended to constitute Incentive Stock
Options shall not constitute Incentive Stock Options to the extent that such
options, in the aggregate, become exercisable for the first time in any one
calendar year for shares of Common Stock with an aggregate fair market value
(determined as of the respective date or dates of grant) of more than $100,000.

     (d)  TERMINATION OF EMPLOYMENT, DEATH OR DISABILITY. No Incentive Stock
Option may be exercised unless, at the time of such exercise, the optionee is,
and has been continuously since the date of grant of his or her option, employed
by the Corporation, its parent, or any subsidiary, except that:

          (i)     an Incentive Stock Option may be exercised within the period
     of three months after the date the optionee ceases to be an employee of the
     Corporation, its parent, or any subsidiary (or within such lesser period as
     may be specified in the applicable option agreement); PROVIDED, that the
     agreement with respect to such option may designate a longer exercise
     period and that he exercise after such three-month period shall be treated
     as the exercise of a non-statutory option under the Plan;

          (ii)    if the optionee dies while in the employ of the Corporation,
     its parent, or any subsidiary, or within three months after the optionee
     ceases to be such an employee, the Incentive Stock Option may be exercised
     by the person to whom it is transferred by will or the laws of descent and
     distribution within the period of one year after the date of death (or
     within such lesser period as may be specified in the applicable option
     agreement); and

          (iii)   if the optionee becomes disabled (within the meaning of
     Section 22(e)(3) of the Code or any successor provision thereto) while in
     the employ of the Corporation, its parent, or any subsidiary, the Incentive
     Stock Option may be exercised within the

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     period of one year after the date the optionee ceases to be such an
     employee because of such disability (or within such lesser period as may be
     specified in the applicable option agreement).

     For all purposes of the Plan and any option granted hereunder, "employment"
shall be defined in accordance with the provisions of Section 1.421-7(h) of the
Income Tax Regulations (or any successor regulations) and shall include
employment by the Corporation, its parent, or any subsidiary. Employment shall
not be deemed to be terminated because an optionee is transferred from one of
the Corporation, its parent, or any subsidiary to another one of the
Corporation, its parent, or any subsidiary. Notwithstanding the foregoing
provisions, no Incentive Stock Option may be exercised after its expiration
date.

     12.  ADDITIONAL PROVISIONS.

     (a)  ADDITIONAL OPTION PROVISIONS. The Board of Directors may, in its sole
discretion, include additional provisions in option agreements covering options
granted under the Plan, including without limitation restrictions on transfer,
repurchase rights, commitments to pay cash bonuses, to make, arrange for or
guaranty loans or to transfer other property to optionees upon exercise of
options, or such other provisions as shall be determined by the Board of
Directors; PROVIDED that such additional provisions shall not be inconsistent
with any other term or condition of the Plan and such additional provisions
shall not cause any Incentive Stock Option granted under the Plan to fail to
qualify as an Incentive Stock Option within the meaning of Section 422 of the
Code.

     (b)  ACCELERATION, EXTENSION, ETC. The Board of Directors may, in its sole
discretion, (i) accelerate the date or dates on which all or any particular
option or options granted under the Plan may be exercised or (ii) extend the
dates during which all, or any particular, option or options granted under the
Plan may be exercised; PROVIDED, HOWEVER, that no such extension shall be
permitted if it would cause the Plan to fail to comply with Section 422 of the
Code.

     13.  GENERAL RESTRICTIONS.

     (a)  INVESTMENT REPRESENTATIONS. The Corporation may require any person to
whom an option is granted, as a condition of exercising such option, to give
written assurances in substance and form satisfactory to the Corporation to the
effect that such person is acquiring the Common Stock subject to the option for
his or her own account for investment and not with any present intention of
selling or otherwise distributing the same, and to such other effects as the
Corporation deems necessary or appropriate in order to comply with federal and
applicable state securities laws, or with covenants or representations made by
the Corporation in connection with any public offering of its Common Stock.

     (b)  COMPLIANCE WITH SECURITIES LAWS. Each option shall be subject to the
requirement that if, at any time, counsel to the Corporation shall determine
that the listing, registration or qualification of the shares subject to such
option upon any securities exchange or under any state or federal law, or the
consent or approval of any governmental or regulatory body, or that the
disclosure of non-public information or the satisfaction of any other condition
is

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necessary as a condition of, or in connection with, the issuance or purchase of
shares thereunder, such option may not be exercised, in whole or in part, unless
such listing, registration, qualification, consent or approval, or satisfaction
of such condition shall have been effected or obtained on conditions acceptable
to the Board of Directors. Nothing herein shall be deemed to require the
Corporation to apply for or to obtain such listing, registration or
qualification, or to satisfy such condition.

     14.  RIGHTS AS A SHAREHOLDER.

     The holder of an option shall have no rights as a shareholder with respect
to any shares covered by the option (including, without limitation, any rights
to receive dividends or non-cash distributions with respect to such shares)
until the date of issue of a stock certificate to him or her for such shares. No
adjustment shall be made for dividends or other rights for which the record date
is prior to the date such stock certificate is issued.

     15.  ADJUSTMENT PROVISIONS FOR RECAPITALIZATIONS AND RELATED TRANSACTIONS.

     (a)  GENERAL. If, through or as a result of any merger, consolidation, sale
of all or substantially all of the assets of the Corporation, reorganization,
recapitalization, reclassification, stock dividend, stock split, reverse stock
split or other similar transaction,

          (i) the outstanding shares of Common Stock are increased, decreased or
     exchanged for a different number or kind of shares or other securities of
     the Corporation, or

          (ii) additional shares or new or different shares or other securities
     of the Corporation or other non-cash assets are distributed with respect to
     such shares of Common Stock or other securities, an appropriate and
     proportionate adjustment shall be made in (x) the maximum number and kind
     of shares reserved for issuance under the Plan, (y) the number and kind of
     shares or other securities subject to any then outstanding options under
     the Plan, and (z) the price for each share subject to any then outstanding
     options under the Plan, without changing the aggregate purchase price as to
     which such options remain exercisable. Notwithstanding the foregoing, no
     adjustment shall be made pursuant to this Section 15 if such adjustment
     would cause the Plan to fail to comply with Section 422 of the Code. If
     this Section 15 applies and Section 16 also applies to any event, then
     Section 16 shall be applicable to such event and this Section 15 shall not
     be applicable.

     (b)  BOARD AUTHORITY TO MAKE ADJUSTMENTS. Any adjustments under this
Section 15 will be made by the Board of Directors, whose determination as to
what adjustments, if any, will be made and the extent thereof will be final,
binding and conclusive. No fractional shares will be issued under the Plan on
account of any such adjustments.

     16.  MERGER, CONSOLIDATION, ASSET SALE, LIQUIDATION, ETC.

     (a)  GENERAL. Subject to Section 16(b), upon the occurrence of an
Acquisition Event

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(as defined below), or the execution by the Corporation of any agreement with
respect to an Acquisition Event, the Board of Directors shall take any one or
more of the following actions with respect to then Outstanding Options (which
term shall include all vested and unvested, but unexercised Options specified in
all issued, outstanding and then currently binding Stock Option Agreements):

          (i) provide that such Outstanding Options shall be assumed, or
     equivalent options shall be substituted, by the acquiring or succeeding
     corporation (or an affiliate thereof), PROVIDED that any such options
     substituted for Outstanding Incentive Stock Options shall meet the
     requirements of Section 424(a) of the Code;

          (ii) upon written notice to the optionees, provide that all then
     unexercised Outstanding Options will become exercisable in full as of a
     specified time (the "Acceleration Time") prior to the Acquisition Event and
     will terminate immediately prior to the consummation of such Acquisition
     Event, except to the extent exercised by the optionees between the
     Acceleration Time and the consummation of such Acquisition Event;

          (iii) in the event of a merger under the terms of which holders of the
     Common Stock of the Corporation will receive upon consummation thereof a
     cash or stock payment for each share surrendered in the merger (the "Merger
     Price"), make or provide for a cash or stock payment to each optionee equal
     to (A) the Merger Price times the number of shares of Common Stock issuable
     to that Optionee upon the exercise by that Optionee of such of that
     Optionee's Outstanding Options (whether or not then exercisable at prices
     not in excess of the Merger Price) which that Optionee actually elects to
     exercise, less (B) the aggregate exercise price of all such Outstanding
     Options which the Optionee actually exercises in exchange for the
     termination of all of that Optionee's Outstanding Options; or

          (iv) provide that all or any Outstanding Options shall become
     exercisable in full immediately prior to such event.

An "Acquisition Event" shall mean: (A) any merger or consolidation which results
in the voting securities of the Corporation outstanding immediately prior
thereto representing immediately thereafter (either by remaining outstanding or
by being converted into voting securities of the surviving or acquiring entity)
less than 50% of the combined voting power of the voting securities of the
Corporation or such surviving or acquiring entity outstanding immediately after
such merger or consolidation, (B) any sale of all or substantially all of the
assets of the Corporation, or (C) the complete liquidation of the Corporation.

     (b)  SUBSTITUTE OPTIONS. The Corporation may grant options under the Plan
in substitution for options held by employees of another corporation who become
employees of the Corporation, or a subsidiary of the Corporation, as the result
of a merger or consolidation of the employing corporation with the Corporation
or a subsidiary of the Corporation, or as a result of the acquisition by the
Corporation, or one of its subsidiaries, of property or stock of the employing
corporation. The Corporation may direct that substitute options be granted on
such

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terms and conditions as the Board of Directors considers appropriate in the
circumstances.

     17.  NO SPECIAL EMPLOYMENT RIGHTS.

     Nothing contained in the Plan or in any option shall confer upon any
optionee any right with respect to the continuation of his or her employment by
the Corporation or interfere in any way with the right of the Corporation at any
time to terminate such employment or to increase or decrease the compensation of
the optionee.

     18.  OTHER EMPLOYEE BENEFITS.

     Except as to plans which by their terms include such amounts as
compensation, the amount of any compensation deemed to be received by an
employee as a result of the exercise of an option or the sale of shares received
upon such exercise will not constitute compensation with respect to which any
other employee benefits of such employee are determined, including, without
limitation, benefits under any bonus, pension, profit-sharing, life insurance or
salary continuation plan, except as otherwise specifically determined by the
Board of Directors.

     19.  AMENDMENT OF THE PLAN.

     (a)  The Board of Directors may at any time, and from time to time, modify
or amend the Plan in any respect, except that if at any time the approval of the
shareholders of the Corporation is required under Section 422 of the Code or any
successor provision with respect to Incentive Stock Options, the Board of
Directors may not effect such modification or amendment without such approval.

     (b)  The termination or any modification or amendment of the Plan shall
not, without the consent of an optionee, affect his or her rights under an
option previously granted to him or her. With the consent of the optionee
affected, the Board of Directors may amend outstanding option agreements in a
manner not inconsistent with the Plan. The Board of Directors shall have the
right to amend or modify the terms and provisions of the Plan and of any
outstanding Incentive Stock Options granted under the Plan to the extent
necessary to qualify any or all such options for such favorable federal income
tax treatment (including deferral of taxation upon exercise) as may be afforded
incentive stock options under Section 422 of the Code.

     20.  WITHHOLDING.

     The Corporation shall have the right to deduct from payments of any kind
otherwise due to the optionee any federal, state or local taxes of any kind
required by law to be withheld with respect to any shares issued upon exercise
of options under the Plan. Subject to the prior approval of the Corporation,
which may be withheld by the Corporation in its sole discretion, the optionee
may elect to satisfy such obligations, in whole or in part,

          (i) by causing the Corporation to withhold shares of Common Stock
     otherwise issuable pursuant to the exercise of an option or

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          (ii) by delivering to the Corporation shares of Common Stock already
     owned by the optionee. The shares so delivered or withheld shall have a
     fair market value equal to such withholding obligation. The fair market
     value of the shares used to satisfy such withholding obligation shall be
     determined by the Corporation as of the date that the amount of tax to be
     withheld is to be determined. An optionee who has made an election pursuant
     to this Section 20(a) may only satisfy his or her withholding obligation
     with shares of Common Stock which are not subject to any repurchase,
     forfeiture, unfulfilled vesting or other similar requirements.

     21.  CANCELLATION AND NEW GRANT OF OPTIONS, ETC.

     The Board of Directors shall have the authority to effect, at any time and
from time to time, with the consent of the affected optionees,

          (i) the cancellation of any or all outstanding options under the Plan
     and the grant in substitution therefor of new options under the Plan
     covering the same or different numbers of shares of Common Stock and having
     an option exercise price per share which may be lower or higher than the
     exercise price per share of the cancelled options, or

          (ii) the amendment of the terms of any and all outstanding options
     under the Plan to provide an option exercise price per share which is
     higher or lower than the then current exercise price per share of such
     outstanding options.

     22.  EFFECTIVE DATE AND DURATION OF THE PLAN.

     (a)  EFFECTIVE DATE. The Plan shall become effective as of the date marked
below, but no Incentive Stock Option granted under the Plan shall become
exercisable unless and until the Plan shall have been approved by the
Corporation's shareholders. If such shareholder approval is not obtained within
twelve months after the effective date of the Plan, no options previously
granted under the Plan shall be deemed to be Incentive Stock Options and no
Incentive Stock Options shall be granted thereafter. Amendments to the Plan not
requiring shareholder approval shall become effective when adopted by the Board
of Directors; amendments requiring shareholder approval (as provided in Section
19) shall become effective when adopted by the Board of Directors, but no
Incentive Stock Option granted after the date of such amendment shall become
exercisable (to the extent that such amendment to the Plan was required to
enable the Corporation to grant such Incentive Stock Option to a particular
optionee) unless and until such amendment shall have been approved by the
Corporation's shareholders. If such shareholder approval is not obtained within
twelve months of the Board's adoption of such amendment, any Incentive Stock
Options granted on or after the date of such amendment shall terminate to the
extent that such amendment to the Plan was required to enable the Corporation to
grant such option to a particular optionee. Subject to this limitation, options
may be granted under the Plan at any time after the effective date and before
the date fixed for termination of the Plan.

     (b)  TERMINATION. Unless sooner terminated in accordance with Section 16,
the Plan shall terminate, with respect to Incentive Stock Options, upon the
earlier of

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          (i) the close of business on the day next preceding the tenth
     anniversary of the date of its adoption by the Board of Directors, or

          (ii) the date on which all shares available for issuance under the
     Plan shall have been issued pursuant to the exercise or cancellation of
     options granted under the Plan. Unless sooner terminated in accordance with
     Section 16, the Plan shall terminate with respect to options which are not
     Incentive Stock Options on the date specified in (ii) above. If the date of
     termination is determined under (i) above, then options outstanding on such
     date shall continue to have force and effect in accordance with the
     provisions of the instruments evidencing such options.

     23.  PROVISION FOR FOREIGN PARTICIPANTS.

     The Board of Directors may, without amending the Plan, modify awards or
options granted to participants who are foreign nationals or employed outside
the United States to recognize differences in laws, rules, regulations or
customs of such foreign jurisdictions with respect to tax, securities, currency,
employee benefit or other matters.

                                            COMBINATORX, INCORPORATED


Effective Date: July 7th, 2000              By: /s/ Alexis Borisy
                                                --------------------------
                                                    Name: Alexis Borisy
                                                    Position: President
                                                    Duly Authorized

                                       10

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                                 AMENDMENT NO. 1

                            COMBINATORX, INCORPORATED

                             2000 STOCK OPTION PLAN


     Reference is hereby made to Section 4 entitled "Stock Subject to Plan" of
the CombinatoRx, Incorporated (hereafter, the "Company") 2000 Stock Option Plan
dated July 7, 2000 (the "Plan").

     Further reference is made to Section 19(a) of the Plan entitled "Amendment
of the Plan" providing for the Board of Directors and Stockholders to amend the
Plan from time to time.

     NOW, THEREFORE, pursuant to written consents of the Board of Directors and
of the Stockholders of the Company dated August 23, 2001, the parties agree as
follows:

     1.      The first sentence of Section No. 4 is deleted in its entirety and
in lieu thereof, there is hereby added the following:

          "Subject to adjustment as provided in Section 15 below, the maximum
          number of shares of Common Stock of the Company which may be issued
          and sold under the Plan is One Million Five Hundred Thousand
          (1,500,000) shares."

     2.      As amended herein, the Plan is hereby ratified, confirmed and
approved in all respects.

     Executed this 23rd day of August, 2001.

                                          COMBINATORX, INCORPORATED


                                          By: /s/ Alexis Borisy
                                              ----------------------------
                                                  Alexis Borisy, President
                                                  Hereunto Duly Authorized

<Page>

                                 AMENDMENT NO. 2

                            COMBINATORX, INCORPORATED

                             2000 STOCK OPTION PLAN

     Reference is hereby made to Section 4 entitled "Stock Subject to Plan" of
the CombinatoRx, Incorporated (hereafter, the "Corporation") 2000 Stock Option
Plan dated July 7, 2000, as previously amended (the "Plan").

     Further reference is made to Section 19(a) of the Plan entitled "Amendment
of the Plan" providing for the Corporation's Board of Directors and Stockholders
to amend the Plan from time to time.

     NOW, THEREFORE, pursuant to that certain Omnibus Consent and Waiver dated
September 10, 2002 executed by the Corporation's Directors and by certain of the
Corporation's Stockholders, the following matters are approved.

     1.      The first sentence of Section 4 of the Plan is deleted in its
entirety and in lieu thereof, there is hereby added the following:

          "Subject to adjustment as provided in Section 15 below, the maximum
          number of shares of Common Stock of the Corporation which may be
          issued and sold under the Plan is Two Million Seven Hundred Thousand
          (2,700,000) shares."

     2.      As amended herein, the Plan is hereby ratified, confirmed and
approved in all respects.

     Executed this 10th day of September, 2002.

                                          COMBINATORX, INCORPORATED


                                          By: /s/ Alexis Borisy
                                              ----------------------------
                                                  Alexis Borisy, President
                                                  Hereunto Duly Authorized

<Page>

                                 AMENDMENT NO. 3

                            COMBINATORX, INCORPORATED

                             2000 STOCK OPTION PLAN


     Reference is hereby made to Section 4 entitled "Stock Subject to Plan" of
the CombinatoRx, Incorporated (hereafter, the "Corporation") 2000 Stock Option
Plan dated July 7, 2000, as previously amended (the "Plan").

     Further reference is made to Section 19(a) of the Plan entitled "Amendment
of the Plan" providing for the Corporation's Board of Directors and Stockholders
to amend the Plan from time to time.

     NOW, THEREFORE, pursuant to that certain Omnibus Consent and Waiver dated
effective February 17, 2004 executed by the Corporation's Directors and by
certain of the Corporation's Stockholders, the following matters are approved.

     1.      The first sentence of Section 4 of the Plan is deleted in its
entirety and in lieu thereof, there is hereby added the following:

          "Subject to adjustment as provided in Section 15 below, the maximum
          number of shares of Common Stock of the Corporation which may be
          issued and sold under the Plan is Three Million Seven Hundred Thousand
          (3,700,000) shares."

     2.      As amended herein, the Plan is hereby ratified, confirmed and
approved in all respects.

     Executed this 28th day of February, 2004.

                                          COMBINATORX, INCORPORATED


                                          By: /s/ Alexis Borisy
                                              ----------------------------
                                                  Alexis Borisy, President
                                                  Hereunto Duly Authorized

<Page>

                                 AMENDMENT NO. 4

                            COMBINATORX, INCORPORATED

                             2000 STOCK OPTION PLAN


     Reference is hereby made to Section 4 entitled "Stock Subject to Plan" of
the CombinatoRx, Incorporated (hereinafter, the "Corporation") 2000 Stock Option
Plan dated July 7, 2000, as previously amended (the "Plan").

     Further reference is made to Section 19(a) of the Plan entitled "Amendment
of the Plan" providing for the Corporation's Board of Directors and Stockholders
to amend the Plan from time to time.

     NOW, THEREFORE, pursuant to that certain Consent dated effective
December 9, 2004 executed by certain of the Corporation's stockholders, the
following matters are approved.

     1.   The first sentence of Section 4 of the Plan is deleted in its entirety
and in lieu thereof, there is hereby added the following:

          "Subject to adjustment as provided in Section 15 below, the maximum
          number of shares of Common Stock of the Corporation which may be
          issued and sold under the Plan is five million three hundred thousand
          (5,300,000) shares."

     2.   As amended herein, the Plan is hereby ratified, confirmed and approved
in all respects.

     Executed this 9th day of December, 2004

                                          COMBINATORX, INCORPORATED


                                          By: /s/ Alexis Borisy
                                             ---------------------------
                                                Alexis Borisy, President
                                                Hereunto Duly Authorized