<Page>

                                                                 Exhibit 10.10

                          REGISTRATION RIGHTS AGREEMENT

     THIS REGISTRATION RIGHTS AGREEMENT is entered into as of April 25, 2001, by
and between Silicon Valley Bank ("Purchaser") and CombinatoRx, Incorporated, a
Delaware corporation (the "Company").

                                    RECITALS

     A.   Concurrently with the execution of this Agreement, Purchaser is
acquiring from the Company a Warrant to Purchase Stock (the "Warrant") pursuant
to which Purchaser has rights to acquire from the Company the Shares (as defined
in the Warrant), which Shares when issued shall be either shares of the
Company's common stock, $.001 par value per share ("Common Stock") or shares
that are convertible into shares of Common Stock ("Conversion Shares").

     B.   By this Agreement, Purchaser and the Company desire to set forth the
registration rights of the Conversion Shares or the Shares all as provided
herein.

          NOW, THEREFORE, in consideration of the premises and the mutual
promises, covenants and conditions hereinafter set forth, the parties hereto
mutually agree as follows:

     1.   REGISTRATION RIGHTS. The Company covenants and agrees as follows:

          1.1    DEFINITIONS. For purposes of this Section 1:

                 (a)     The term "register," "registered," and "registration"
refer to a registration effected by preparing and filing a registration
statement or similar document in compliance with the Securities Act of 1933, as
amended, and the rules and regulations thereunder (the "Securities Act"), and
the declaration or ordering of effectiveness of such registration statement or
document;

                 (b)     The term "Registrable Securities" means (i) (A) the
Conversion Shares, or (B) Shares, at any time when the Shares are shares of
Common Stock, and (ii) any Common Stock or other Securities of the Company
issued as (or issuable upon the conversion or exercise of any warrant, right or
other security which is issued as) a dividend or other distribution with respect
to, or in exchange for or in replacement of, the Shares or Conversion Shares.

                 (c)     The terms "Holder" or "Holders" means Purchaser and its
qualifying transferees under subsection 1.9 hereof who hold Registrable
Securities.

                 (d)     The term "SEC" means the Securities and Exchange
Commission.

                 (e)     The terms "Form S-l," "Form S-3" etc. shall mean those
forms with such designations as are required by the SEC and any successor or
replacement forms adopted by the SEC.

          1.2    COMPANY REGISTRATION.

                 (a)     REGISTRATION. If at any time or from time to time, the
Company shall determine to register any of its securities, for its own account
or the account of any of its shareholders, other than a registration on Form S-8
relating solely to employee stock option or purchase plans or on Form S-4
relating solely to an SEC Rule 145 transaction, the Company will:

<Page>

                         (i)    promptly give to each Holder written notice
thereof (which shall include a list of the jurisdictions in which the Company
intends to attempt to qualify such securities under the applicable blue sky or
other state securities laws); and

                         (ii)   include in such registration (and
qualifications), and in any underwriting involved therein, all the Registrable
Securities specified in a written request or requests, made within 30 days after
receipt of such written notice from the Company, by any Holder or Holders,
except as set forth in subsection 1.2(c) below.

                 (b)     UNDERWRITING. If the registration of which the Company
gives notice is for a registered public offering involving a firm-commitment
underwriting, the Company shall so advise the Holders as a part of the written
notice given pursuant to subsection 1.2(a)(i). In such event the right of any
Holder to registration pursuant to this subsection 1.2 shall be conditioned upon
such Holder's participation in such underwriting and the inclusion of such
Holder's Registrable Securities in the underwriting to the extent provided
herein. All Holders proposing to distribute their securities through such
underwriting shall (together with the Company and the other shareholders
distributing their securities through such underwriting) enter into an
underwriting agreement in customary form (and not inconsistent with the terms
hereof) with the underwriter or underwriters selected for such underwriting by
the Company.

                 (c)     In the case of any registration of Common Stock by the
Company in a firm-commitment underwriting, if the managing underwriters give
written advice to the Company that marketing factors require a limitation on the
number of shares of Common Stock (or other securities convertible into or
exercisable or exchangeable for Common Stock) to be offered and sold by
stockholders of Company in such offering, there shall be included in the
offering: (i) first, all securities proposed by Company to be sold for its
account; and (ii) second, that number of shares of Common Stock, if any,
requested to be included in such registration statement by Holders and by
stockholders of the Company having contractual rights to include shares in such
registration ("Stockholders"), on a pro rata basis based upon the number of
shares of Common Stock each Holder and each such Stockholder beneficially owns.

          1.3    REGISTRATION ON FORM S-3. If at any time (i) the Holder of
Registrable Securities requests in writing that the Company file a registration
statement on Form S-3 or any successor thereto for a public offering of all or
any portion of the shares of Registrable Securities held by the requesting
Holder, (ii) the aggregate price to the public of such offering would reasonably
be expected to exceed $200,000, and (iii) the Company is a registrant entitled
to use Form S-3 or any successor thereto to register such shares, then the
Company shall use its best efforts to register under the Securities Act on
Form S-3 or any successor thereto, for public sale in accordance with the method
of disposition specified in such notice, the number of shares of Registrable
Securities specified in such notice. Whenever the Company is required by this
Section 1.3 to use its best efforts to effect the registration of Registrable
Securities, each of the procedures and requirements of Sections 1.5(d) and 1.8
(as applicable) shall apply to such registration; PROVIDED, HOWEVER, that the
Company shall not be obligated to register Registrable Securities under this
Section 1.3 (x) on more than one occasion in any six-month period, (y) if
Form S-3 is not available for such offering, or (z) if the Company shall furnish
a certificate signed by the chief executive officer stating that in the good
faith judgment of the Company's Board, it would be seriously detrimental to the
Company to effect an S-3 registration at the requested time, in which event the
Company can defer the requested S-3 registration for up to sixty (60) days in
any twelve (12) month period; provided, however, that the Company shall not
utilize this right more than once in any twelve (12) month period.

          1.4    Expenses of Registration. All expenses incurred in connection
with any registration. qualification or compliance pursuant to this Section 1
including without limitation, all registration, filing and qualification fees,
printing expenses, underwriting fees, discounts and commissions, fees and
disbursements of counsel for the Company and expenses of any special audits
incidental to or required by such registration, shall be borne by the Company.
All expenses of any registered offering not otherwise borne by the Company

                                       -2-
<Page>

will be borne pro rata among the Holders, any other shareholders of the Company
participating in such offering and the Company.

          1.5   REGISTRATION PROCEDURES. In the case of each registration,
qualification or compliance effected by the Company pursuant to this
Registration Rights Agreement, the Company will keep each Holder participating
therein advised in writing as to the initiation of each registration,
qualification and compliance and as to the completion thereof. At its expense
the Company will:

                 (a)     Prepare and file with the SEC a registration statement
with respect to such Registrable Securities and use its best efforts to cause
such registration statement to become effective, and, upon the request of the
Holders of a majority of the Registrable Securities registered thereunder, keep
such registration statement effective for up to 120 days (the "Effective
Period").

                 (b)     Prepare and file with the SEC such amendments and
supplements to such registration statement and the prospectus used in connection
with such registration statement as may be necessary to comply with the
provisions of the Securities Act with respect to the disposition of all
securities covered by such registration statement.

                 (c)     Furnish to the Holders such numbers of copies of a
prospectus, including a preliminary prospectus, in conformity with the
requirements of the Securities Act, and such other documents as they may
reasonably request in order to facilitate the disposition of Registrable
Securities covered owned by them.

                 (d)     Use its best efforts to register and qualify the
securities covered by such registration statement under such other securities or
Blue Sky laws of such jurisdictions as shall be reasonably requested by the
Holders, provided that the Company shall not be required in connection therewith
or as a condition thereto to qualify to do business or to file a general consent
to service of process in any states or jurisdictions.

                 (e)     In the event of any underwritten public offering, enter
into and perform its obligations under an underwriting agreement, in usual and
customary form, with the managing underwriter of such offering. Each Holder
participating in such underwriting shall also enter into and perform its
obligations under such an agreement provided that all other shareholders of the
Company participating in such offering do the same.

                 (f)     Notify each Holder of Registrable Securities covered by
such registration statement at any time when a prospectus relating thereto is
required to be delivered under the Securities Act or the happening of any event
as a result of which the prospectus included in such registration statement, as
then in effect, includes an untrue statement of a material fact or omits to
state a material fact required to be stated therein or necessary to make the
statements therein not misleading in the light of the circumstances then
existing.

          1.6    INDEMNIFICATION.

                 (a)     The Company will indemnify each Holder of Registrable
Securities and each of its officers, directors and partners, and each person
controlling such Holder within the meaning of Section 15 of the Securities Act
("controlling person"), and each underwriter, if any, and each controlling
person of such underwriter, with respect to which registration, qualification or
compliance of Registrable Securities has been effected pursuant to this
Registration Rights Agreement, against all claims, losses, expenses, damages and
liabilities (or actions in respect thereto) arising out of or based on any
untrue statement (or alleged untrue statement) of a material fact contained in
any prospectus, offering circular or other document including any related
registration statement, notification or the like) incident to any such
registration,

                                       -3-
<Page>

qualification or compliance, or based on any omission (or alleged omission) to
state therein a material fact required to be stated therein or necessary to make
the statement therein not misleading, or any violation or alleged violation by
the Company of the Securities Act, the Securities Exchange Act of 1934, as
amended, and the rules and regulations thereunder ("Exchange Act") or any state
securities law applicable to the Company or any rule or regulation promulgated
under any such state law and relating to action or inaction required of the
Company in connection with any such registration, qualification or compliance,
and will reimburse each such Holder, each of its officers, directors and
partners, and each person controlling such Holder, each such underwriter and
each person who controls any such underwriter, within a reasonable amount of
time after incurred for any reasonable legal and any other expenses incurred in
connection with, investigating, defending or settling any such claim, loss,
damage, liability or action; PROVIDED, HOWEVER, that the indemnity agreement
contained in this subsection 1.6(a) shall not apply to amounts paid in
settlement of any such claim, loss, damage, liability, or action if such
settlement is effected without the consent of the Company (which consent shall
not be unreasonably withheld or delayed); AND PROVIDED FURTHER, that the Company
will not be liable in any such case to the extent that any such claim, loss,
damage or liability arises out of or is based on any untrue statement or
omission to state a material fact required to be stated or necessary to make a
statement not misleading made in reliance upon and conformity with written
information furnished to the Company by an instrument duly executed by such
Holder specifically for use therein.

                 (b)     Each Holder will, if Registrable Securities held by or
issuable to such Holder are included in the securities as to which such
registration, qualification or compliance is being effected, indemnify the
Company, each of its directors, officers and controlling persons, each
underwriter, if any, of the Company's securities covered by such a registration
statement, and each controlling person of such underwriter, and each other
Holder and Stockholder, each of their officers, directors, partners and
controlling persons, against all claims, losses, expenses, damages and
liabilities (or actions in respect thereof) arising out of or based on any
untrue statement (or alleged untrue statement) of a material fact contained in
any such registration statement, prospectus, offering circular or other
document, or any omission (or alleged omission) to state therein a material fact
required to be stated therein or necessary to make the statements therein not
misleading or any violation by the Holder, its directors, officers, and/or
controlling persons of the Securities Act, the Exchange Act, or any applicable
state securities law or rule or regulation promulgated thereunder, and will
reimburse the Company, such Stockholders, such Holders, such directors,
officers, partners, persons or underwriters for any reasonable legal or any
other expenses incurred in connection with investigating, defending or settling
any such claim, loss, damage, liability or action, in each case to the extent,
but only to the extent, that such untrue statement (or alleged untrue statement)
or omission (or alleged omission) is made in such registration statement,
prospectus, offering circular or other document in reliance upon and in
conformity with written information furnished to the Company by an instrument
duly executed by such Holder specifically for use therein; PROVIDED, HOWEVER,
that the indemnity agreement contained in this subsection 1.6(b) shall not apply
to amounts paid in settlement of any such claim, loss, damage, liability or
action if such settlement is effected without the consent of the Holder, (which
consent shall not be unreasonably withheld or delayed); AND PROVIDED FURTHER,
that the total amount for which any Holder shall be liable under this subsection
1.6(b) shall not in any event exceed the aggregate proceeds received by such
Holder from the sale of Registrable Securities held by such Holder in such
registration.

                 (c)     Each party entitled to indemnification under this
subsection 1.6 (the "Indemnified Party") shall give notice to the party required
to provide indemnification (the "Indemnifying Party") promptly after such
Indemnified Party has actual knowledge of any claim as to which indemnity may be
sought, and shall permit the Indemnifying Party to assume the defense of any
such claim or any litigation, resulting therefrom; provided that counsel for the
Indemnifying Party, who shall conduct the defense of such claim or litigation,
shall be approved by the Indemnified Party (whose approval shall not be
unreasonably withheld), and the Indemnified Party may participate in such
defense at such party's expense; and provided further, that the failure of any
Indemnified Party to give notice as provided herein shall not relieve the
Indemnifying Party of its obligations hereunder, unless such failure resulted in
prejudice to the Indemnifying Party; and provided further, that an Indemnified
Party (together with all other Indemnified Parties which may

                                       -4-
<Page>

be represented without conflict by one counsel) shall have the right to retain
one separate counsel, with the fees and expenses to be paid by the Indemnifying
Party, if representation of such Indemnified Party by the counsel retained by
the Indemnifying Party would be inappropriate due to actual or potential
differing interests between such Indemnified Party and any other party
represented by such counsel in such proceeding. No Indemnifying Party, in the
defense of any such claim or litigation, shall, except with the consent of each
Indemnified Party, consent to entry of any judgment or enter into any settlement
which does not include as an unconditional term thereof the giving by the
claimant or plaintiff to such Indemnified Party of a release from all liability
in respect to such claim or litigation.

          1.7    INFORMATION BY HOLDER. Any Holder or Holders of Registrable
Securities included in any registration shall promptly furnish to the Company
such information regarding such Holder or Holders and the distribution proposed
by such Holder or Holders as the Company may request in writing and as shall be
required in connection with any registration, qualification or compliance
referred to herein.

          1.8    RULE 144 REPORTING AND FORM S-3. With a view to making
available to Holders the benefits of certain rules and regulations of the SEC
which may permit the sale of the Registrable Securities to the public without
registration or pursuant to a registration on Form S-3, the Company agrees at
all times to:

                 (a)     make and keep public information available, as those
terms are understood and defined in SEC Rule 144, after 90 days after the
effective date of the first registration filed by the Company for an offering of
its securities to the general public;

                 (b)     take such action, including the voluntary registration
of its Common Stock under Section 12 of the Exchange Act, as is necessary to
enable the Holders to utilize Form S-3 for the sale of their Registrable
Securities, such action to be taken as soon as practicable after the end of the
fiscal year in which the first registration statement filed by the Company for
the offering of its securities to the general public is declared effective;

                 (c)     file with the SEC in a timely manner all reports and
other documents required of the Company under the Securities Act and the
Exchange Act (at any time after it has become subject to such reporting
requirements); and

                 (d)     so long as a Holder owns any Registrable Securities, to
furnish to such Holder forthwith upon request a written statement by the Company
as to its compliance with the reporting requirements of said Rule 144 (at any
time after 90 days after the effective date of the first registration statement
filed by the Company for an offering of its securities to the general public),
and of the Securities Act and the Exchange Act (at any time after it has become
subject to such reporting requirements), or that it qualifies as a registrant
whose securities may be resold pursuant to S-3 (at any time after it so
qualifies), a copy of the most recent annual or quarterly report of the Company,
and such other reports and documents so filed by the Company as the Holder may
reasonably request in complying with any rule or regulation of the SEC allowing
the Holder to sell any such securities without registration or pursuant to such
form.

          1.9    TRANSFER OF REGISTRATION RIGHTS. Holders' rights to cause the
Company to register their securities and keep information available, granted to
them by the Company under subsections 1.2, 1.3 and 1.8 may be assigned to a
transferee or assignee of a Holder's Registrable Securities not sold to the
public, provided, that the Company is given written notice by such Holder at the
time of or within a reasonable time after said transfer, stating the name and
address of said transferee or assignee and identifying the securities with
respect to which such registration rights are being assigned.

          1.10   MARKET STAND-OFF AGREEMENT. Each Holder hereby agrees that,
during the period of duration specified by the Company and an underwriter of
Common Stock or other securities of the

                                       -5-
<Page>

Company, following the effective date of a registration statement of the Company
filed under the Securities Act, it shall not, to the extent requested by the
Company and such underwriter, directly or indirectly, sell, offer to sell,
contract to sell, grant any option to purchase or otherwise transfer or dispose
of (other than to donees who agree to be similarly bound) any securities of the
Company held by it at any time during such period except Common Stock included
in such registration; provided, however, that:

                 (a)     such restriction shall be applicable only to the first
such registration statement of the Company which covers Common Stock (or other
securities) to be sold on its behalf to the public in an underwritten offering;

                 (b)     such market stand-off time period shall not exceed 180
days;

                 (c)     all officers and directors of the Company and all other
holders of at least 1% of the shares of Common Stock outstanding immediately
prior to such registration enter into similar agreements; and

                 (d)     such market stand-off agreement shall be terminated and
be of no further, force and effect if any Holder, Stockholder, or any officer or
director of the Company or any such 1% holder bound by a similar agreement is
released or otherwise no longer bound by the provisions hereof or thereof and
the Company shall upon request of a Holder certify to such Holder whether or not
it has granted any such release.

     In order to enforce the foregoing covenant, the Company may impose stop
transfer instructions with respect to the Registrable Securities of each Holder
and Stockholder (and the shares of securities of every other person subject to
the foregoing restriction) until the end of such period.

     Notwithstanding the foregoing, the obligations described in this
Section 1.10 shall not apply to a registration relating solely to employee
benefit plans on Form S-l or Form S-8 or similar forms which may be promulgated
in the future, or a registration relating solely to a Commission Rule 145
transaction on Form S-14 or form S-15 or similar forms which may be promulgated
in the future.

          1.11   TERMINATION OF REGISTRATION RIGHTS. No Holder shall be entitled
to exercise any right provided for in this Section 1 after seven (7) years
following the consummation of the sale of securities pursuant to a registration
statement filed by the Company under the Act in connection with the initial firm
commitment underwritten offering of its securities to the general public.

     2.   GENERAL.

          2.1    WAIVERS AND AMENDMENTS. With the written consent of the record
or beneficial holders of at least 50.1% of the Registrable Securities, the
obligations of the Company and the rights of the Holders of the Registrable
Securities under this agreement may be waived (either generally or in a
particular instance, either retroactively or prospectively, and either for a
specified period of time or indefinitely), and with the same consent the
Company, when authorized by resolution of its Board of Directors, may enter into
a supplementary agreement for the purpose of adding any provisions to or
changing in any manner or eliminating any of the provisions of this Agreement;
provided, however, that no such modification, amendment or waiver shall reduce
the aforesaid percentage of Registrable Securities without the consent of all
of the Holders of the Registrable Securities. Upon the effectuation of each such
waiver, consent, agreement of amendment or modification, the Company shall
promptly give written notice thereof to the record holders of the Registrable
Securities who have, not previously consented thereto in writing. This Agreement
or any provision hereof may be changed, waived, discharged or terminated only by
a statement in writing signed by the party against which enforcement of the
change, waiver, discharge or termination is. sought, except to the extent
provided in this subsection 2.1.

                                       -6-
<Page>

          2.2    GOVERNING LAW. This Agreement shall be governed in all respects
by the laws of Commonwealth of Massachusetts as such laws are applied to
agreements between Massachusetts residents entered into and to be performed
entirely within Massachusetts.

          2.3    SUCCESSORS AND ASSIGNS. Except as otherwise expressly provided
herein, the provisions hereof shall inure to the benefit of, and be
binding upon, the successors, assigns, heirs, executors and administrators of
the parties hereto.

          2.4    ENTIRE AGREEMENT. Except as set forth below, this Agreement and
the other documents delivered pursuant hereto constitute the full and entire
understanding and agreement between the parties with regard to the subjects
hereof and thereof.

          2.5    NOTICES, ETC. All notices and other communications required or
permitted hereunder shall be in writing and shall be mailed by first class mail,
postage prepaid, certified or registered mail, return receipt requested, or
reputable overnight courier, addressed (a) if to Holder, at such Holder's
address(es) as set forth below, or at such other address(es) as such Holder
shall have furnished to the Company in writing, or(b) if to the Company, at the
Company's address set forth below, or at such other address as the Company shall
have furnished to the Holder in writing.

          2.6    SEVERABILITY. In case any provision of this Agreement shall be
invalid, illegal, or unenforceable, the validity, legality and enforceability
of the remaining provisions of this Agreement or any provision of the other
Agreement s shall not in any way be affected or impaired thereby.

          2.7.   TITLES AND SUBTITLES. The titles of the sections and
subsections of this Agreement are for convenience of reference only and are not
to be considered in construing this Agreement.

          2.8    COUNTERPARTS. This Agreement may be executed in any number of
counterparts, each of which shall be an original, but all of which together
shall constitute one instrument.


PURCHASERS                                      COMPANY

SILICON VALLEY BANK                             COMBINATORX, INCORPORATED.

By: /s/ Laura M. Scott                          By: /s/ Alexis Borisy
   ----------------------------                    ----------------------------
Name: Laura M. Scott                            Name: Alexis Borisy
     --------------------------                      --------------------------
Title: Vice President                           Title: President
      -------------------------                       -------------------------
Address:                                        Address:
        -----------------------
        -----------------------

copy to:  Silicon Valley Bank
          Treasury Department
          3003 Tasman Drive, HA-200
          Santa Clara, CA 95054

                                       -7-