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                                                                   Exhibit 10.10

                               INDEMNITY AGREEMENT


        THIS INDEMNITY AGREEMENT, effective as of June 20, 2000 between Applied
Molecular Evolution, Inc., a Delaware corporation (the "Corporation"), and
________________ (the "Indemnitee"),

                              W I T N E S S E T H:

        Whereas Indemnitee is a member of the board of directors of the
Corporation (the "Board of Directors") and/or is an officer of the Corporation
and in such capacity is performing a valuable service for the Corporation; and

        Whereas Indemnitee is willing to serve, continue to serve, and take on
additional service for or on behalf of the Corporation on the condition that he
be indemnified as herein provided; and

        Whereas it is intended that Indemnitee shall be paid promptly by the
Corporation all amounts necessary to effectuate in full the indemnity provided
herein.

        N o w, T h e r e f o r e, in consideration of the premises and the
covenants in this Agreement, and intending to be legally bound hereby, the
parties hereto agree as follows:

        1. Services by Indemnitee.

               Indemnitee agrees to serve as a director and/or officer of the
Corporation so long as he is duly appointed or elected and qualified in
accordance with the applicable provisions of the Restated Certificate of
Incorporation and By-laws of the Corporation or any subsidiary of the
Corporation and until such time as he resigns or fails to stand for election or
is removed from his position. Indemnitee may at any time and for any reason
resign or be removed from such position (subject to any other contractual
obligation or other obligation imposed by operation of law), in which event the
Corporation shall have no obligation under this Agreement to continue Indemnitee
in any such position.

        2. Indemnification.

               (a) The Corporation shall indemnify Indemnitee against Expenses
and Liabilities in connection with any Proceeding arising out of acts or
omissions of Indemnitee in his capacity as a director and/or an officer of the
Corporation occurring subsequent to the date hereof to the fullest extent
permitted by applicable law or the Restated Certificate of Incorporation of the
Corporation in effect on the date hereof or as such law or Restated Certificate
of Incorporation may from time to time be amended (but, in the case of any such
amendment, only to the extent such amendment permits the Corporation to provide
broader indemnification rights than the law or Restated Certificate of
Incorporation permitted the Corporation to provide before such amendment). The
right to indemnification provided in the Restated Certificate of Incorporation
shall be presumed to have been relied upon by Indemnitee


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in serving or continuing to serve the Corporation and shall be enforceable as a
contract right. Without diminishing the scope of the indemnification provided by
this Section 2, the Corporation shall indemnify Indemnitee whenever he is or was
a party or is threatened to be made a party to any Proceeding, including without
limitation any such Proceeding brought by or in the right of the Corporation,
because he is or was a director and/or officer of the Corporation or because of
anything done or not done by him in such capacity, against Expenses and
Liabilities actually and reasonably incurred by Indemnitee or on his behalf in
connection with such Proceeding, including the costs of any investigation,
defense, settlement or appeal, except that no indemnification shall be made with
respect to any claim, issue or matter if Indemnitee was finally adjudged to be
liable to the Corporation by a court of competent jurisdiction due to his gross
negligence or willful misconduct unless and to the extent that a Delaware Court
of Chancery or the court in which the action was heard determines that
Indemnitee is entitled to indemnification for such amounts as the court deems
proper. In addition to, and not as a limitation of, the foregoing, the rights of
indemnification of Indemnitee provided under this Agreement shall include those
rights set forth in Sections 3, 7, 8 and 12 below.

               (b) Indemnitee shall be paid promptly by the Corporation all
amounts necessary to effectuate the foregoing indemnity.

        3. Advancement of Expenses.

               All reasonable Expenses incurred by or on behalf of Indemnitee
shall be advanced from time to time by the Corporation to him within thirty (30)
days after the Corporation's receipt of a written request for an advance of
Expenses, whether prior to or after final disposition of a Proceeding (except to
the extent that there has been a Final Adverse Determination that Indemnitee is
not entitled to be indemnified for such Expenses), including without limitation
any Proceeding brought by or in the right of the Corporation. The written
request for an advancement of any and all Expenses under this paragraph shall
contain reasonable detail of the Expenses incurred by Indemnitee. If required by
law at the time of such advance, Indemnitee hereby agrees to repay the amounts
advanced if it is ultimately determined that Indemnitee is not entitled to be
indemnified pursuant to the terms of this Agreement.

        4. Limitations.

               The foregoing indemnity and advancement of Expenses shall apply
only to the extent that Indemnitee has not been indemnified and reimbursed
pursuant to such insurance as the Corporation may maintain for Indemnitee's
benefit, or otherwise; provided, however, that notwithstanding the availability
of such other indemnification and reimbursement, Indemnitee may claim
indemnification and advancement of Expenses pursuant to this Agreement by
assigning to the Corporation, at its request, Indemnitee's claims under such
insurance to the extent Indemnitee has been paid by the Corporation.

        5. Insurance and Funding.

               The Corporation may purchase and maintain insurance to protect
itself and/or Indemnitee against any Expenses and Liabilities in connection with
any Proceeding to the fullest extent permitted by applicable laws. The
Corporation may create a trust fund, grant an interest


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or use other means (including, without limitation, a letter of credit) to ensure
the payment of such amounts as may be necessary to effect indemnification or
advancement of Expenses as provided in this Agreement.

        6. Procedure for Determination of Entitlement to Indemnification.

               (a) Whenever Indemnitee believes that he is entitled to
indemnification pursuant to this Agreement, Indemnitee shall submit a written
request for indemnification to the Corporation. Any request for indemnification
shall include sufficient documentation or information reasonably available to
Indemnitee to support his claim for indemnification. Indemnitee shall submit his
claim for indemnification within a reasonable time not to exceed five years
after any judgment, order, settlement, dismissal, arbitration award, conviction,
acceptance of a plea of nolo contendere or its equivalent, final termination or
other disposition or partial disposition of any Proceeding, whichever is the
later date for which Indemnitee requests indemnification. The President or the
Secretary or other appropriate officer shall, promptly upon receipt of
Indemnitee's request for indemnification, advise the Board of Directors in
writing that Indemnitee has made such request. Determination of Indemnitee's
entitlement to indemnification shall be made not later than ninety (90) days
after the Corporation's receipt of Indemnitee's written request for such
indemnification.

               (b) The Indemnitee shall be entitled to select the forum in which
Indemnitee's request for indemnification will be heard, which selection shall be
included in the written request for indemnification required in Section 6(a).
The forum shall be any one of the following:

               (i) The stockholders of the Corporation;

               (ii) A quorum of the Board of Directors consisting of
        Disinterested Directors;

               (iii) Independent Legal Counsel, who shall make the determination
        in a written opinion; or

               (iv) A panel of three arbitrators, one selected by the
        Corporation, another by Indemnitee and the third by the first two
        arbitrators selected. If for any reason three arbitrators are not
        selected within thirty (30) days after the appointment of the first
        arbitrator, then selection of additional arbitrators shall be made by
        the American Arbitration Association. If any arbitrator resigns or is
        unable to serve in such capacity for any reason, the American
        Arbitration Association shall select his replacement. The arbitration
        shall be conducted pursuant to the commercial arbitration rules of the
        American Arbitration Association now in effect.

               If Indemnitee fails to make such designation, his claim shall be
determined by an appropriate court of the State of Delaware.


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        7. Fees and Expenses of Independent Legal Counsel.

               The Corporation agrees to pay the reasonable fees and expenses of
Independent Legal Counsel or a panel of three arbitrators should such Counsel or
such panel of arbitrators be retained to make a determination of Indemnitee's
entitlement to indemnification pursuant to Section 6 of this Agreement, and to
fully indemnify such Counsel or arbitrators against any and all expenses and
losses incurred by any of them arising out of or relating to this Agreement or
their engagement pursuant hereto.

        8. Remedies of Indemnitee.

               (a) In the event that (i) a determination pursuant to Section 6
hereof is made that Indemnitee is not entitled to indemnification, (ii) advances
of Expenses are not made pursuant to this Agreement, (iii) payment has not been
timely made following a determination of entitlement to indemnification pursuant
to this Agreement, or (iv) Indemnitee otherwise seeks enforcement of this
Agreement, Indemnitee shall be entitled to a final adjudication in an
appropriate court of the State of Delaware of his rights. Alternatively,
Indemnitee at his option may seek an award in arbitration to be conducted by a
single arbitrator pursuant to the commercial arbitration rules of the American
Arbitration Association now in effect, whose decision is to be made within
ninety (90) days following the filing of the demand for arbitration. The
Corporation shall not oppose Indemnitee's right to seek any such adjudication or
arbitration award.

               (b) In the event that a determination that Indemnitee is not
entitled to indemnification, in whole or in part, has been made pursuant to
Section 6 hereof, the decision in the judicial proceeding or arbitration
provided in paragraph (a) of this Section 8 shall be made de novo and Indemnitee
shall not be prejudiced by reason of a determination that he is not entitled to
indemnification.

               (c) If a determination that Indemnitee is entitled to
indemnification has been made pursuant to Section 6 hereof or otherwise pursuant
to the terms of this Agreement, the Corporation shall be bound by such
determination in the absence of (i) a misrepresentation of a material fact by
Indemnitee or (ii) a specific finding (which has become final) by an appropriate
court of the State of Delaware that all or any part of such indemnification is
expressly prohibited by law.

               (d) In any court proceeding pursuant to this Section 8, the
Corporation shall be precluded from asserting that the procedures and
presumptions of this Agreement are not valid, binding and enforceable. The
Corporation shall stipulate in any such court or before any such arbitrator that
the Corporation is bound by all the provisions of this Agreement and is
precluded from making any assertion to the contrary.

               (e) Expenses reasonably incurred by Indemnitee in connection with
his request for indemnification under this Agreement, seeking enforcement of
this Agreement or to recover damages for breach of this Agreement shall be borne
by the Corporation.


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        9. Modification, Waiver, Termination and Cancellation.

               No supplement, modification, termination, cancellation or
amendment of this Agreement shall be binding unless executed in writing by both
of the parties hereto. No waiver of any of the provisions of this Agreement
shall be deemed or shall constitute a waiver of any other provisions hereof
(whether or not similar), nor shall such waiver constitute a continuing waiver.

        10. Notice by Indemnitee and Defense of Claim.

               Indemnitee shall promptly notify the Corporation in writing upon
being served with any summons, citation, subpoena, complaint, indictment,
information or other document relating to any matter, whether civil, criminal,
administrative or investigative, but the omission so to notify the Corporation
will not relieve it from any liability which it may have to Indemnitee if such
omission does not prejudice the Corporation's rights. If such omission does
prejudice the Corporation's rights, the Corporation will be relieved from
liability only to the extent of such prejudice; nor will such omission relieve
the Corporation from any liability which it may have to Indemnitee otherwise
than under this Agreement. With respect to any Proceeding as to which Indemnitee
notifies the Corporation of the commencement thereof:

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

               (b) The Corporation jointly with any other indemnifying party
similarly notified will be entitled to assume the defense thereof, with counsel
reasonably satisfactory to Indemnitee; provided, however, that the Corporation
shall not be entitled to assume the defense of any Proceeding if Indemnitee
shall have reasonably concluded that there may be a conflict of interest between
the Corporation and Indemnitee with respect to such Proceeding. After notice
from the Corporation to Indemnitee of its election to assume the defense
thereof, the Corporation will not be liable to Indemnitee under this Agreement
for any Expenses subsequently incurred by Indemnitee in connection with the
defense thereof, other than reasonable costs of investigation or as otherwise
provided below. Indemnitee shall have the right to employ Indemnitee's own
counsel in such Proceeding but the fees and expenses of such counsel incurred
after notice from the Corporation of its assumption of the defense thereof shall
be at the expense of Indemnitee unless:

               (i) The employment of counsel by Indemnitee has been authorized
        by the Corporation;

               (ii) Indemnitee shall have reasonably concluded that counsel
        engaged by the Corporation may not adequately represent Indemnitee;

               (iii) The Corporation shall not in fact have employed counsel to
        assume the defense in such Proceeding or shall not in fact have assumed
        such defense and be acting in connection therewith with reasonable
        diligence;

               in each of which cases the fees and expenses of such counsel
shall be at the expense of the Corporation.


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               (c) The Corporation shall not settle any Proceeding in any manner
which would impose any penalty or limitation on Indemnitee without Indemnitee's
written consent; provided, however, that Indemnitee will not unreasonably
withhold his consent to any proposed settlement.

        11. Notices.

               All notices, requests, demands and other communications hereunder
shall be in writing and shall be deemed to have been duly given if (i) delivered
by hand and receipted for by the party to whom said notice or other
communication shall have been directed, or (ii) mailed by certified or
registered mail with postage prepaid, on the third business day after the date
on which it is so mailed:

               (a) If to Indemnitee, to:




or to such other address as may have been furnished to Indemnitee

               (b) If to the Corporation, to:

                      Applied Molecular Evolution, Inc.
                      3520 Dunhill Street
                      San Diego, California 92121
                      Attn: Chief Executive Officer

or to such other address as may have been furnished to Indemnitee by the
Corporation or to the Corporation by Indemnitee, as the case may be.

        12. Nonexclusivity.

               The rights of Indemnitee hereunder shall not be deemed exclusive
of any other rights to which Indemnitee may now or in the future be entitled
under the Delaware General Corporation Law, the Corporation's Restated
Certificate of Incorporation or By-laws, or any agreements, vote of
stockholders, resolution of the Board of Directors or otherwise.

        13. Certain Definitions.

               (a) "Disinterested Director" shall mean a director of the
Corporation who is not or was not a party to the Proceeding in respect of which
indemnification is being sought by Indemnitee.

               (b) "Expenses" shall include all direct and indirect costs
(including, without limitation, attorneys' fees, retainers, court costs,
transcripts, fees of experts, witness fees, travel expenses, duplicating costs,
printing and binding costs, telephone charges, postage, delivery service fees,
all other disbursements or out-of-pocket expenses and reasonable compensation
for time spent by Indemnitee for which he is otherwise not compensated by the
Corporation)


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actually and reasonably incurred in connection with a Proceeding or establishing
or enforcing a right to indemnification under this Agreement, applicable law or
otherwise; provided, however, that "Expenses" shall not include any Liabilities.

               (c) "Final Adverse Determination" shall mean that a determination
that Indemnitee is not entitled to indemnification shall have been made pursuant
to Section 6 hereof and either (i) a final adjudication in a Delaware court or
decision of an arbitrator pursuant to Section 8(a) hereof shall have denied
Indemnitee's right to indemnification hereunder, or (ii) Indemnitee shall have
failed to file a complaint in a Delaware court or seek an arbitrator's award
pursuant to Section 8(a) for a period of one hundred twenty (120) days after the
determination made pursuant to Section 6 hereof.

               (d) "Indemnification Period" shall mean the period of time during
which Indemnitee shall continue to serve as a director and/or as an officer of
the Corporation, and thereafter so long as Indemnitee shall be subject to any
possible Proceeding arising out of acts or omissions of Indemnitee as a director
and/or as an officer of the Corporation.

               (e) "Independent Legal Counsel" shall mean a law firm or a member
of a law firm selected by the Corporation and approved by Indemnitee (which
approval shall not be unreasonably withheld) and that neither is presently nor
in the past five years has been retained to represent: (i) the Corporation, in
any material matter, or (ii) any other party to the Proceeding giving rise to a
claim for indemnification hereunder. Notwithstanding the foregoing, the term
"Independent Legal Counsel" shall not include any person who, under the
applicable standards of professional conduct then prevailing, would have a
conflict of interest in representing either the Corporation or Indemnitee in an
action to determine Indemnitee's right to indemnification under this Agreement.

               (f) "Liabilities" shall mean liabilities of any type whatsoever
including, but not limited to, any judgments, fines, ERISA excise taxes and
penalties, penalties and amounts paid in settlement (including all interest
assessments and other charges paid or payable in connection with or in respect
of such judgments, fines, penalties or amounts paid in settlement) of any
proceeding.

               (g) "Proceeding" shall mean any threatened, pending or completed
action, claim, suit, arbitration, alternate dispute resolution mechanism,
investigation, administrative hearing or any other proceeding whether civil,
criminal, administrative or investigative, including any appeal therefrom.

        14. Binding Effect, Duration and Scope of Agreement.

               This Agreement shall be binding upon and inure to the benefit of
and be enforceable by the parties hereto and their respective successors and
assigns (including any direct or indirect successor by purchase, merger,
consolidation or otherwise to all or substantially all of the business or assets
of the Corporation), spouses, heirs and personal and legal representatives. This
Agreement shall continue in effect during the Indemnification Period, regardless
of whether Indemnitee continues to serve as a director and/or officer.


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        15. Severability.

               If any provision or provisions of this Agreement (or any portion
thereof) shall be held to be invalid, illegal or unenforceable for any reason
whatsoever:

               (a) The validity, legality and enforceability of the remaining
provisions of this Agreement shall not in any way be affected or impaired
thereby; and

               (b) To the fullest extent legally possible, the provisions of
this Agreement shall be construed so as to give effect to the intent of any
provision held invalid, illegal or unenforceable.

        16. Governing Law and Interpretation of Agreement.

               This Agreement shall be governed by and construed and enforced in
accordance with the laws of the State of Delaware, as applied to contracts
between Delaware residents entered into and to be performed entirely within
Delaware. If the laws of the State of Delaware are hereafter amended to permit
the Corporation to provide broader indemnification rights than said laws
permitted the Corporation to provide prior to such amendment, the rights of
indemnification and advancement of expenses conferred by this Agreement shall
automatically be broadened to the fullest extent permitted by the laws of the
State of Delaware, as so amended.

        17. Consent to Jurisdiction.

               The Corporation and Indemnitee each irrevocably consent to the
jurisdiction of the courts of the State of Delaware for all purposes in
connection with any action or proceeding which arises out of or relates to this
Agreement and agree that any action instituted under this Agreement shall be
brought only in the state courts of the State of Delaware.

        18. Entire Agreement.

               This Agreement represents the entire agreement between the
parties hereto, and there are no other agreements, contracts or understandings
between the parties hereto with respect to the subject matter of this Agreement,
except as specifically referred to herein or as provided in Section 12 hereof.


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        19. 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 one and the same Agreement.

               Executed this ____ day of June, 2000.

                                          APPLIED MOLECULAR EVOLUTION, INC.



                                          By
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                                          INDEMNITEE



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