<Page>
Exhibit 10.4
Nonstatutory Stock Option
Granted Under 2004 Incentive Plan of CombinatoRx, Incorporated
--------------------------------------------------------------
1. GRANT OF OPTION.
This certificate evidences a nonstatutory stock option (this "Stock
Option") granted by CombinatoRx, Incorporated, a Delaware corporation (the
"Company"), on [________] to [____________] (the "Participant") pursuant to the
Company's 2004 Incentive Plan (as from time to time in effect, the "Plan").
Under this Stock Option, the Participant may purchase, in whole or in part, on
the terms herein provided, a total of [___] shares of common stock of the
Company (the "Shares") at $[_____] per Share. The latest date on which this
Stock Option, or any part thereof, may be exercised is [_________] (the "Final
Exercise Date"). The Stock Option evidenced by this certificate is intended to
be, and is hereby designated, a nonstatutory option, that is, an option that
does NOT qualify as an incentive stock option as defined in section 422 of the
Internal Revenue Code of 1986, as amended from time to time (the "Code").
This Stock Option is exercisable in the following cumulative installments
prior to the Final Exercise Date:
[_______] Shares on and after [___________________, 20__];
and an additional [_______] Shares on and after each quarterly
anniversary thereafter, starting on [___________________, 20__].
Notwithstanding the foregoing, upon termination of the Participant's Employment,
any portion of this Stock Option that is not then exercisable will promptly
expire and the remainder of this Stock Option will remain exercisable for three
months; PROVIDED, that any portion of this Stock Option held by the Participant
immediately prior to the Participant's death, to the extent then exercisable,
will remain exercisable for one year following the Participant's death; AND
FURTHER PROVIDED, that in no event shall any portion of this Stock Option be
exercisable after the Final Exercise Date.
2. EXERCISE OF STOCK OPTION.
Each election to exercise this Stock Option shall be in writing, signed by
the Participant or the Participant's executor, administrator, or legally
appointed representative (in the event of the Participant's incapacity) or the
person or persons to whom this Stock Option is transferred by will or the
applicable laws of descent and distribution (collectively, the "Option Holder"),
and received by the Company at its principal office, accompanied by this
certificate and payment in full as provided in the Plan. Subject to the further
terms and conditions provided in the Plan, the purchase price may be paid as
follows: (i) by delivery of cash or check acceptable to the Administrator; (ii)
through a broker-assisted exercise program acceptable to the Administrator;
(iii) through the delivery of Shares that have been outstanding for at least six
months (unless the Administrator provides a shorter period) and that have a fair
market value equal to the exercise price, (iv) by other means acceptable to the
Administrator, or (v) through any combination of the foregoing. In the event
that this Stock Option is exercised by an Option Holder other than the
-1-
<Page>
Participant, the Company will be under no obligation to deliver Shares hereunder
unless and until it is satisfied as to the authority of the Option Holder to
exercise this Stock Option.
3. RESTRICTIONS ON TRANSFER OF SHARES.
If at the time this Stock Option is exercised the Company or any of its
shareholders is a party to any agreement restricting the transfer of any
outstanding shares of the Company's common stock, the Administrator may provide
that this Stock Option may be exercised only if the Shares so acquired are made
subject to the transfer restrictions set forth in that agreement (or if more
than one such agreement is then in effect, the agreement or agreements specified
by the Administrator).
4. WITHHOLDING; AGREEMENT TO PROVIDE SECURITY.
If at the time this Stock Option is exercised the Company determines that
under applicable law and regulations it could be liable for the withholding of
any federal or state tax upon exercise or with respect to a disposition of any
Shares acquired upon exercise of this Stock Option, this Stock Option may not be
exercised unless the person exercising this Stock Option remits to the Company
any amounts determined by the Company to be required to be withheld upon
exercise (or makes other arrangements satisfactory to the Company for the
payment of such taxes).
5. NONTRANSFERABILITY OF STOCK OPTION.
This Stock Option is not transferable by the Participant otherwise than by
will or the laws of descent and distribution, and is exercisable during the
Participant's lifetime only by the Participant (or in the event of the
Participant's incapacity, the person or persons legally appointed to act on the
Participant's behalf).
6. PROVISIONS OF THE PLAN.
This Stock Option is subject to the provisions of the Plan, which are
incorporated herein by reference. A copy of the Plan as in effect on the date of
the grant of this Stock Option has been furnished to the Participant. By
exercising all or any part of this Stock Option, the Participant agrees to be
bound by the terms of the Plan and this certificate. All initially capitalized
terms used herein will have the meaning specified in the Plan, unless another
meaning is specified herein.
-2-
<Page>
IN WITNESS WHEREOF, the Company has caused this instrument to be executed
by its duly authorized officer.
COMBINATORX, INCORPORATED
By
----------------------------
Dated: [_________________]
Acknowledged
----------------------------
[NAME OF PARTICIPANT]
Dated: [_________________]
-3-