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                                                                    Exhibit 10.1


                            INDEMNIFICATION AGREEMENT


         THIS AGREEMENT is made and entered into this ____ day of _____________,
_____  between Senomyx, Inc., a Delaware corporation ("Corporation"), and
___________ ("Agent").


                                    RECITALS

         A.       Agent will serve, at the will of Corporation or under separate
contract, if any such contract exists, as director, officer or other fiduciary
of Corporation (including any employee benefit plan of Corporation) faithfully
and to the best of Agent's ability so long as Agent is duly elected and
qualified in accordance with the provisions of the Bylaws or other applicable
charter documents of Corporation; PROVIDED, HOWEVER, that Agent may at any time
and for any reason resign from such position (subject to any contractual
obligation that Agent may have assumed apart from this Agreement) and that
Corporation shall have no obligation under this Agreement to continue Agent in
any such position; and

         B.       The stockholders of Corporation have adopted Bylaws (the
"Bylaws") providing for the indemnification of the officers, directors, agents
and employees of Corporation to the maximum extent authorized by the Delaware
General Corporations Law, as amended (the "DGCL"); and

         C.       The Bylaws and the DGCL, by their non-exclusive nature, permit
contracts between Corporation and its agents with respect to indemnification of
such agents; and

         D.       In accordance with the authorization as provided by the DGCL,
Corporation has purchased and presently maintains a policy or policies of
Directors and Officers Liability Insurance ("D & O Insurance"), covering certain
liabilities which may be incurred by its officers and directors in their
performance as agents of Corporation; and

         E.       As a result of developments affecting the terms, scope and
availability of D & O Insurance there exists general uncertainty as to the
extent of protection afforded its agents by such D & O Insurance and by
statutory and bylaw indemnification provisions; and

         F.       In order to induce Agent to continue to serve in such
capacity, Corporation has determined and agreed to enter into this Agreement
with Agent.

         NOW, THEREFORE, in consideration of Agent's continued service as an
officer or director after the date hereof, the parties hereto agree as follows:


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                                    AGREEMENT

         1.       INDEMNITY OF AGENT. Corporation hereby agrees to hold harmless
and indemnify Agent to the fullest extent authorized or permitted by the
provisions of the Bylaws and the DGCL, as the same may be amended from time to
time but, only to the extent that such amendment permits Corporation to provide
broader indemnification rights than the Bylaws or the DGCL permitted prior to
adoption of such amendment).

         2.       ADDITIONAL INDEMNITY. Subject only to the exclusions set forth
in Section 3 hereof, Corporation hereby further agrees to hold harmless and
indemnify Agent:

                  (a)      against any and all expenses (including attorneys'
fees), witness fees, judgments, fines and amounts paid in settlement actually
and reasonably incurred by Agent in connection with any threatened, pending or
completed action, suit or proceeding, whether civil, criminal, administrative or
investigative (including an action by or in the right of Corporation) to which
Agent is, was or at any time becomes a party, or is threatened to be made a
party, by reason of the fact that Agent is, was or at any time becomes a
director, officer, employee or agent of Corporation, or is or was serving or at
any time serves at the request of Corporation as a director, officer, employee
or agent of another corporation, partnership, joint venture, trust, employee
benefit plan or other enterprise; and

                  (b)      otherwise to the fullest extent as may be provided to
Agent by Corporation under the non-exclusivity provisions of Article XI, Section
43 of the Bylaws of Corporation and the DGCL.

         3.       LIMITATIONS ON ADDITIONAL INDEMNITY. No indemnity pursuant to
Section 2 hereof shall be paid by Corporation:

                  (a)      except to the extent the aggregate of losses to be
indemnified thereunder exceeds the sum of such losses for which Agent is
indemnified pursuant to Section 1 hereof or pursuant to any D & O Insurance
purchased and maintained by Corporation;

                  (b)      in respect to remuneration paid to Agent if it shall
be determined by a final judgment or other final adjudication that such
remuneration was in violation of law;

                  (c)      on account of any claim against Agent for an
accounting of profits made from the purchase or sale by Agent of securities of
Corporation pursuant to the provisions of Section 16(b) of the Securities
Exchange Act of 1934 and amendments thereto or similar provisions of any
federal, state or local statutory law;


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                  (d)      on account of Agent's conduct that is established by
a final judgment to have been knowingly fraudulent or deliberately dishonest, or
to constitute willful misconduct;

                  (e)      on account of Agent's conduct that is established by
a final judgment as constituting a breach of Agent's duty of loyalty to
Corporation or resulting in any personal profit or advantage to which Agent was
not legally entitled;

                  (f)      for which payment is actually made to Agent under a
valid and collectible insurance policy or under a valid and enforceable
indemnity clause, bylaw or agreement, except in respect of any excess beyond
payment under such insurance, clause, bylaw or agreement;

                  (g)      on account of any action, claim or proceeding
initiated by Agent unless (i) such action, claim or proceeding was authorized in
the specific case by action of the Board of Directors, (ii) such indemnification
is expressly required to be made by law, (iii) such indemnification is provided
by Corporation, in its sole discretion, pursuant to the powers vested in
Corporation under the DGCL, or (iv) the proceeding is initiated pursuant to
Section 9(b) hereof; or

                  (h)      if such indemnification is not lawful (and, in this
respect, both Corporation and Agent have been advised that the Securities and
Exchange Commission believes that indemnification for liabilities arising under
the federal securities laws is against public policy and is, therefore,
unenforceable and that claims for indemnification should be submitted to
appropriate courts for adjudication).

         4.       CONTRIBUTION. If the indemnification provided in Sections 1
and 2 hereof is unavailable by reason of a Court decision described in Section
3(h) hereof based on grounds other than any of those set forth in paragraphs (b)
through (g) of Section 3 hereof, then in respect of any threatened, pending or
completed action, suit or proceeding in which Corporation is jointly liable with
Agent (or would be if joined in such action, suit or proceeding), Corporation
shall contribute to the amount of expenses (including attorneys' fees),
judgments, fines and amounts paid in settlement actually and reasonably incurred
and paid or payable by Agent in such proportion as is appropriate to reflect (i)
the relative benefits received by Corporation on the one hand and Agent on the
other hand from the transaction from which such action, suit or proceeding
arose, and (ii) the relative fault of Corporation on the one hand and of Agent
on the other in connection with the events which resulted in such expenses,
judgments, fines or settlement amounts, as well as any other relevant equitable
considerations. The relative fault of Corporation on the one hand and of Agent
on the other shall be determined by reference to, among other things, the
parties' relative intent, knowledge, access to information and opportunity to
correct or prevent the circumstances resulting in such expenses, judgments,
fines or settlement amounts. Corporation agrees that it would not be just and
equitable if contribution pursuant to this Section 4 were determined by pro rata
allocation or any other method of allocation that does not take account of the
foregoing equitable considerations.


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         5.       CONTINUATION OF OBLIGATIONS. All agreements and obligations of
Corporation contained herein shall continue during the period Agent is a
director, officer, employee or other fiduciary of Corporation (or is or was
serving at the request of Corporation as a director, officer, employee or agent
of another corporation, partnership, joint venture, trust, employee benefit plan
or other enterprise) and shall continue thereafter so long as Agent shall be
subject to any possible claim or threatened, pending or completed action, suit
or proceeding, whether civil, criminal, arbitrational, administrative, or
investigative, by reason of the fact that Agent was an officer or director of
Corporation or serving in any other capacity referred to herein.

         6.       PARTIAL INDEMNIFICATION. Agent shall be entitled under this
Agreement to indemnification by Corporation for a portion of the expenses
(including attorneys' fees), witness fees, damages, judgments, fines and amounts
paid in settlement and any other amounts that Agent becomes legally obligated to
pay in connection with any action, suit or proceeding referred to in Section 2
hereof even if not entitled hereunder to indemnification for the total amount
thereof, and Corporation shall indemnify Agent for the portion thereof to which
Agent is entitled.

         7.       NOTIFICATION AND DEFENSE OF CLAIM. Not later than thirty (30)
days after receipt by Agent of notice of the commencement of any action, suit or
proceeding, Agent will, if a claim in respect thereof is to be made against
Corporation under this Agreement, notify Corporation of the commencement
thereof; but the omission so to notify Corporation will not relieve it from any
liability which it may have to Agent otherwise than under this Agreement. With
respect to any such action, suit or proceeding as to which Agent notifies
Corporation of the commencement thereof:

                  (a)      Corporation will be entitled to participate therein
at its own expense;

                  (b)      except as otherwise provided below, to the extent
that it may wish, Corporation jointly with any other indemnifying party
similarly notified will be entitled to assume the defense thereof, with counsel
reasonably satisfactory to Agent. After notice from Corporation to Agent of its
election so as to assume the defense thereof, Corporation will not be liable to
Agent under this Agreement for any legal or other expenses subsequently incurred
by Agent in connection with the defense thereof other than reasonable costs of
investigation or as otherwise provided below. Agent shall have the right to
employ its counsel in such action, suit or proceeding but the fees and expenses
of such counsel incurred after notice from Corporation of its assumption of the
defense thereof shall be at the expense of Agent unless (i) the employment of
counsel by Agent has been authorized by Corporation, (ii) Agent shall have
reasonably concluded, and shall have so notified Corporation, that there is an
actual conflict of interest between Corporation and Agent in the conduct of the
defense of such action, or (iii) Corporation shall not in fact have employed
counsel to assume the defense of such action, in each of which cases the fees
and expenses of Agent's separate counsel shall be at the expense of Corporation.
Corporation shall not be entitled to assume the defense of any action, suit or
proceeding brought by or on behalf of Corporation or as to which Agent shall
have made the conclusion provided for in (ii) above; and


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                  (c)      Corporation shall not be liable to indemnify Agent
under this Agreement for any amounts paid in settlement of any action or claim
effected without Corporation's written consent. Corporation shall be permitted
to settle any action except that it shall not settle any action or claim in any
manner that would impose any penalty or limitation on Agent without Agent's
written consent. Neither Corporation nor Agent will unreasonably withhold its
consent to any proposed settlement.

         8.       EXPENSES. The Corporation shall advance, prior to the final
dispositions of any proceeding, promptly following request therefore, all
expenses incurred by Agent in connection with such proceeding upon receipt of an
undertaking by or on behalf of Agent to repay said amounts if it shall be
determined ultimately that Agent is not entitled to be indemnified under the
provisions of this Agreement, the Bylaws, the DGCL or otherwise.

         9.       ENFORCEMENT.

                  (a)      Corporation expressly confirms and agrees that it has
entered into this Agreement and assumed the obligations imposed on Corporation
hereby in order to induce Agent to continue as an officer or director of
Corporation, and acknowledges that Agent is relying upon this Agreement in
continuing in such capacity.

                  (b)      Any right to indemnification or advances granted by
this Agreement to Agent shall be enforceable by or on behalf of Agent in any
court of competent jurisdiction if (i) the claim for indemnification or advances
is denied, in whole or in part, or (ii) no disposition of such claim is made
within ninety (90) days of request therefor. Agent, in such enforcement action,
if successful in whole or in part, shall be entitled to be paid also the expense
of prosecuting his claim. It shall be a defense to any action for which a claim
for indemnification is made under Section 2 hereof (other than an action brought
to enforce a claim for expenses pursuant to Section 8 hereof, PROVIDED THAT the
required undertaking has been tendered to Corporation) that Agent is not
entitled to indemnification because of the limitations set forth in Section 3
hereof. Neither the failure of Corporation (including its Board of Directors or
its stockholders) to have made a determination prior to the commencement of such
enforcement action that indemnification of Agent is proper in the circumstances,
nor an actual determination by Corporation (including its Board of Directors or
its stockholders) that such indemnification is improper shall be a defense to
the action or create a presumption that Agent is not entitled to indemnification
under this Agreement or otherwise.

         10.      SUBROGATION. In the event of payment under this agreement,
Corporation shall be subrogated to the extent of such payment to all of the
rights of recovery of Agent, who shall execute all documents required and shall
do all acts that may be necessary to secure such rights and to enable
Corporation effectively to bring suit to enforce such rights.


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         11.      NON-EXCLUSIVITY OF RIGHTS. The rights conferred on Agent by
this Agreement shall not be exclusive of any other right which Agent may have or
hereafter acquire under any statute, provision of Corporation's Certificate of
Incorporation or Bylaws, agreement, vote of stockholders or directors, or
otherwise, both as to action in his official capacity and as to action in
another capacity while holding office.

         12.      SURVIVAL OF RIGHTS.

                  (a)      The rights conferred on Agent by this Agreement shall
continued after Agent has ceased to be a director, officer, employee or other
agent of Corporation or to serve at the request of Corporation as a director,
officer, employee or other agent of another corporation, partnership, joint
venture, trust, employee benefit plan or other enterprise and shall inure to the
benefit of Agent's heirs, executors and administrators.

                  (b)      Corporation shall require any successor (whether
director or indirect, by purchase, merger, consolidation or otherwise) to all or
substantially all of the business or assets of Corporation, expressly to assume
and agree to perform this Agreement in the same manner and to the same extent
that Corporation would be required to perform if no such succession had taken
place.

         13.      SEPARABILITY. Each of the provisions of this Agreement is a
separate and distinct agreement and independent of the others, so that if any or
all of the provisions hereof shall be held to be invalid or unenforceable for
any reason, such invalidity or unenforceability shall not affect the validity or
enforceability of the other provisions hereof or the obligation of the
Corporation to indemnify the Agent to the full extent provided by the Bylaws or
the DGCL.

         14.      GOVERNING LAW. This Agreement shall be interpreted and
enforced in accordance with the laws of the State of Delaware.

         15.      BINDING EFFECT. This Agreement shall be binding upon Agent and
upon Corporation, its successors and assigns, and shall inure to the benefit of
Agent, Agent's heirs, personal representatives and assigns and to the benefit of
Corporation, its successors and assigns.

         16.      AMENDMENT AND TERMINATION. No amendment, modification,
termination or cancellation of this Agreement shall be effective unless in
writing signed by both parties hereto.

         17.      IDENTICAL COUNTERPARTS. This Agreement may be executed in one
or more counterparts, each of which shall for all purposes be deemed to be an
original but all of which together shall constitute but one and the same
Agreement. Only one such counterpart need be produced to evidence the existence
of this Agreement.


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         18.      HEADINGS. The headings of the sections of this Agreement are
inserted for convenience only and shall not be deemed to constitute part of this
Agreement or affect the construction hereof.

         19.      NOTICES. All notices, requests, demands and other
communications hereunder shall be in writing and shall be deemed to have been
duly given (i) upon delivery if delivered by hand to the party to whom such
communication was directed or (ii) upon the third business day after the date on
which such communication was mailed if mailed by certified or registered mail
with postage prepaid:

                  (a)      If to Agent, at the address indicated on the
signature page hereof.

                  (b)      If to Corporation, to:

                           Senomyx, Inc.
                           11099 North Torrey Pines Road
                           La Jolla, CA 92037
                           Attention:  Corporate Counsel

         IN WITNESS WHEREOF, the parties hereto have executed this Agreement on
and as of the day and year first above written.

                                      SENOMYX, INC.



                                      By:
                                          --------------------------------------
                                          Paul Grayson
                                          PRESIDENT AND CHIEF EXECUTIVE OFFICER

                                      AGENT



                                      By:
                                          --------------------------------------

                                      Name:
                                            ------------------------------------

                                      Address:
                                               ---------------------------------


Senomyx Legal Dept. Approval:


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