<PAGE>
                                                                    Exhibit 10.1

                                     FORM OF

                            INDEMNIFICATION AGREEMENT

            This Indemnification Agreement, is entered into this _____ day of
__________, _____ ("Agreement"), by and between Stratagene Corporation, a
Delaware corporation ("Company"), and ______________ ("Indemnitee").

            WHEREAS, highly competent persons are becoming more reluctant to
serve corporations as directors or in other capacities unless they are provided
with adequate protection through insurance or adequate indemnification against
risks of claims and actions against them arising out of their service to and
activities on behalf of the corporation;

            WHEREAS, the current impracticability of obtaining adequate
insurance and the uncertainties relating to indemnification have increased the
difficulty of attracting and retaining such persons;

            WHEREAS, the Board of Directors of the Company (the "Board") has
determined that the inability to attract and retain such persons is detrimental
to the best interests of the Company's stockholders and that the Company should
act to assure such persons that there will be increased certainty of such
protection in the future;

            WHEREAS, it is reasonable, prudent and necessary for the Company
contractually to obligate itself to indemnify such persons as provided herein so
that they will serve or continue to serve the Company free from undue concern
that they will not be so indemnified; and

            WHEREAS, Indemnitee is willing to serve, continue to serve and to
take on additional service for or on behalf of the Company on the condition that
he or she be so indemnified.

            NOW, THEREFORE, in consideration of the premises and the covenants
contained herein, the Company and Indemnitee do hereby covenant and agree as
follows:

            Section 1. Services by Indemnitee. Indemnitee agrees to serve as an
officer or director of the Company. Indemnitee may at any time and for any
reason resign from such position (subject to any other contractual obligation or
any obligation imposed by operation of law). The Company shall have no
obligation under this Agreement to continue Indemnitee in any position with the
Company.

            Section 2. Indemnification -- General. The Company shall indemnify,
and pay Expenses (as hereinafter defined) to Indemnitee, as provided in this
Agreement and to the fullest extent required by applicable law in effect on the
date hereof and to such greater extent as applicable law may thereafter from
time to time require.

            Section 3. Proceedings Other Than Proceedings by or in the Right of
the Company. Indemnitee shall be entitled to the rights of indemnification
provided in this Section 3
<PAGE>
if, by reason of his or her Corporate Status (as hereinafter defined), he or she
is, or is threatened to be made, a party to any threatened, pending or completed
Proceeding (as hereinafter defined), other than a Proceeding by or in the right
of the Company in which indemnification is not permitted as a matter of law.
Pursuant to this Section 3, Indemnitee shall be indemnified against Expenses,
judgments, penalties, fines and amounts paid in settlement actually and
reasonably incurred by him or her or on his or her behalf in connection with
such Proceeding or any claim, issue or matter therein, if he or she acted in
good faith and in a manner he or she reasonably believed to be in or not opposed
to the best interests of the Company, and, with respect to any criminal
Proceeding, did not knowingly behave in an unlawful manner.

            Section 4. Proceedings by or in the Right of the Company. Indemnitee
shall be entitled to the rights of indemnification provided in this Section 4
if, by reason of his or her Corporate Status, he or she is, or is threatened to
be made, a party to any threatened, pending or completed Proceeding brought by
or in the right of the Company to procure a judgment in its favor. Pursuant to
this Section, Indemnitee shall be indemnified against Expenses actually and
reasonably incurred by him or her or on his or her behalf in connection with
such Proceeding if he or she acted in good faith and in a manner he or she
reasonably believed to be in or not opposed to the best interests of the
Company. Notwithstanding the foregoing, no indemnification against such Expenses
shall be made in respect of any claim, issue or matter in such Proceeding as to
which Indemnitee shall have been adjudged to be liable to the Company.

            Section 5. Indemnification for Expenses of a Party Who is Wholly or
Partly Successful. To the extent that Indemnitee is, by reason of his or her
Corporate Status, a party to and is successful, on the merits or otherwise, in
any Proceeding, he or she shall be indemnified against all Expenses actually and
reasonably incurred by him or her or on his or her behalf in connection
therewith. If Indemnitee is not wholly successful in such Proceeding but is
successful, on the merits or otherwise, as to one or more but less than all
claims, issues or matters in such Proceeding, the Company shall indemnify
Indemnitee against all Expenses actually and reasonably incurred by him or her
or on his or her behalf in connection with each successfully resolved claim,
issue or matter. For purposes of this Section and without limitation, the
termination of any claim, issue or matter in such a Proceeding by dismissal,
with or without prejudice, shall be deemed to be a successful result as to such
claim, issue or matter.

            Section 6. Indemnification for Expenses of a Witness. To the extent
that Indemnitee is, by reason of his or her Corporate Status, a witness in any
Proceeding, he or she shall be indemnified against all Expenses actually and
reasonably incurred by him or her or on his or her behalf in connection
therewith.

            Section 7. Notification and Defense of Claims. Not later than thirty
(30) days after receipt by Indemnitee of notice of the commencement of any
action, suit or proceeding, Indemnitee will, if a claim in respect thereof is to
be made against the Company under this Agreement, notify the Company in writing
of the commencement thereof; but the omission to so notify the Company will not
relieve the Company from any liability which it may have to Indemnitee otherwise
than under this Agreement. With respect to any such action, suit or proceeding
as to which Indemnitee notifies the Company of the commencement thereof:

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


                                       2
<PAGE>
            (b) except as otherwise provided below, to the extent that it may
wish, the Company jointly with any other indemnifying party similarly notified
will be entitled to assume the defense thereof, with counsel reasonably
satisfactory to Indemnitee. After notice from the Company to Indemnitee of its
election to assume the defense thereof, the Company will not be liable to
Indemnitee under this Agreement for any legal or other expenses subsequently
incurred by Indemnitee in connection with the defense thereof other than as
otherwise provided below. Indemnitee shall have the right to employ its counsel
in such action, suit or proceeding but all Expenses incurred shall be at the
expense of Indemnitee unless: (i) the employment of counsel by Indemnitee has
been authorized in writing by the Chief Executive Officer of the Company or his
designee; (ii) the Company and its counsel shall each have determined in their
reasonable discretion that there is a meaningful conflict of interest between
the Company and Indemnitee in the conduct of the defense of such action and the
Company does not retain an independent second counsel to represent Indemnitee;
or (iii) the Company shall have refused to employ counsel to assume the defense
of such action within thirty (30) days after proper notice has been received, in
each of which cases the fees and expenses of Indemnitee's separate counsel shall
be at the expense of the Company only until the Company elects to assume or
resume the defense of Indemnitee. The Company shall not be obligated to pay for
the reasonable fees and expenses of more than one separate counsel to represent
Indemnitee and all other indemnitees; and

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

            Section 8. Payment and Repayment of Expenses

            (a) In the event that Indemnitee employs his or her own counsel
pursuant to Section 7(b)(i) through (iii) above, the Company shall pay
Indemnitee, prior to any final disposition of any threatened or pending action,
suit or proceeding, whether civil, criminal, administrative or investigative,
any and all reasonable third-party Expenses (including attorneys' fees )
incurred in investigating or defending any such action, suit or proceeding
within thirty (30) days after the receipt by the Company of a statement or
statements from Indemnitee requesting such payment from time to time, whether
prior to or after final disposition of such Proceeding. Such statement or
statements shall reasonably evidence the third-party Expenses incurred by
Indemnitee in detail and shall include or be preceded or accompanied by an
undertaking by or on behalf of Indemnitee to repay any Expenses paid by the
Company if it shall ultimately be determined that Indemnitee is not entitled to
be indemnified against such Expenses. Notwithstanding anything to the contrary
in this Agreement, the Company shall not be required to pay such expenses to
Indemnitee in connection with any action, suit or proceeding brought by the
Company and approved by a majority of the Board of Directors which alleges
willful misappropriation of corporate assets by Indemnitee or any other willful
and deliberate breach in bad faith of Indemnitee's duty to the Company or its
stockholders. Indemnitee hereby agrees to assign to the Company all claims and
other rights to take legal action, and hereby grants to the Company a
power-of-attorney to proceed, against any provider of services for which the
Company has paid or is obligated to pay related Expenses hereunder.


                                       3
<PAGE>
            (b) Indemnitee agrees that Indemnitee will reimburse the Company for
all reasonable expenses paid by the Company in defending any action, suit or
proceeding against Indemnitee in the event and only to the extent it shall be
ultimately determined by a final judicial decision (from which there is no right
of appeal) that Indemnitee is not entitled, under applicable law, the Company's
Bylaws, this Agreement or otherwise, to be indemnified by the Company for such
expenses.

            Section 9. Remedies of Indemnitee; Effect of Certain Proceedings

            (a) In the event that (i) payment of Expenses is not timely made
pursuant to Section 8 of this Agreement or (ii) payment of indemnification is
not made pursuant to Sections 3, 4, 5 or 6 of this Agreement within thirty (30)
days after receipt by the Company of a written request therefor, Indemnitee
shall be entitled to an adjudication in an appropriate court of the State of
Delaware, or in any other court of competent jurisdiction, of his or her
entitlement to such indemnification of Expenses. Indemnitee shall commence such
proceeding seeking an adjudication within 180 days following the date on which
Indemnitee first has the right to commence such proceeding pursuant to this
Section 9(a). The Company shall not oppose Indemnitee's right to seek any such
adjudication.

            (b) In the event that Indemnitee, pursuant to this Section 9, seeks
a judicial adjudication to enforce his or her rights under, or to recover
damages for breach of, this Agreement, Indemnitee shall be entitled to recover
from the Company, and shall be indemnified by the Company against, any and all
expenses (of the types described in the definition of Expenses in Section 16 of
this Agreement) actually and reasonably incurred by him or her in such judicial
adjudication, but only if he or she prevails therein. If it shall be determined
in said judicial adjudication that Indemnitee is entitled to receive part but
not all of the indemnification of expenses sought, the expenses incurred by
Indemnitee in connection with such judicial adjudication shall be appropriately
prorated.

            (c) The termination of any Proceeding or of any claim, issue or
matter therein, by judgment, order, settlement or conviction, or upon a plea of
nolo contendere or its equivalent, shall not (except as otherwise expressly
provided in this Agreement) of itself adversely affect the right of Indemnitee
to indemnification or create a presumption that Indemnitee did not act in good
faith and in a manner which he or she reasonably believed to be in or not
opposed to the best interests of the Company or, with respect to any criminal
Proceeding, was unlawful.

            Section 10. Non-Exclusivity; Survival of Rights; Insurance;
Subrogation

            (a) The rights of indemnification and to receive payment of Expenses
as provided by this Agreement shall not be deemed exclusive of any other rights
which may be required under applicable law, any agreement, a vote of
stockholders or a resolution of directors, or otherwise.

            (b) To the extent that the Company maintains an insurance policy or
policies providing liability insurance for directors, officers, employees,
agents or fiduciaries of the Company or of any other corporation, partnership,
joint venture, trust, employee benefit plan or other enterprise which such
person serves at the request of the Company, Indemnitee shall be


                                       4
<PAGE>
covered by such policy or policies in accordance with its or their terms to the
extent of the coverage available for any such director, officer, employee, agent
or fiduciary under such policy or policies.

            (c) In the event of any payment under this Agreement, the Company
shall be subrogated to the extent of such payment to all of the rights of
recovery of Indemnitee, who shall execute all papers required and take all
action necessary to secure such rights, including execution of such documents as
are necessary to enable the Company to bring suit to enforce such rights.

            (d) The Company shall not be liable under this Agreement to make any
payment of amounts otherwise indemnifiable hereunder if and to the extent that
Indemnitee has otherwise actually received such payment under any insurance
policy, contract, agreement or otherwise.

            (e) The Company may, to the full extent authorized by law, create a
trust fund, grant a security interest and/or use other means (including, without
limitation, letters of credit, surety bonds and other similar arrangements) to
ensure the payment of such amounts as may become necessary or desirable to
effect indemnification provided hereunder.

            Section 11. Duration of Agreement. This Agreement shall continue
until and terminate upon the later of: (a) ten (10) years after the date that
Indemnitee shall have ceased to serve as a director, officer, employee, agent or
fiduciary of the Company or of any other corporation, partnership, joint
venture, trust, employee benefit plan or other enterprise which Indemnitee
served at the request of the Company; or (b) the final termination of all
pending Proceedings in respect of which Indemnitee is granted rights of
indemnification of expenses hereunder and of any proceeding commenced by
Indemnitee pursuant to Section 9 of this Agreement relating thereto. This
Agreement shall be binding upon the Company and its successors and assigns and
shall inure to the benefit of Indemnitee and his or her heirs, executors and
administrators.

            Section 12. Severability. If any provision or provisions of this
Agreement 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 (including, without limitation, each portion of any
Section of this Agreement containing any such provision held to be invalid,
illegal or unenforceable, that is not itself invalid, illegal or unenforceable)
shall not in any way be affected or impaired thereby; and (b) to the fullest
extent possible, the provisions of this Agreement (including, without
limitation, each portion of any Section of this Agreement containing any such
provision held to be invalid, illegal or unenforceable, that is not itself
invalid, illegal or unenforceable) shall be construed so as to give effect to
the intent manifested by the provision held invalid, illegal or unenforceable.

            Section 13. Exception to Right of Indemnification or Payment of
Expenses. Notwithstanding any other provision of this Agreement, Indemnitee
shall not be entitled to indemnification of Expenses under this Agreement with
respect to any Proceeding, or any claim therein, brought or made by him or her
against the Company.


                                       5
<PAGE>
            Section 14. 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 one and the same
Agreement. Only one such counterpart signed by the party against whom
enforceability is sought needs to be produced to evidence the existence of this
Agreement.

            Section 15. Headings. The headings of the paragraphs of this
Agreement are inserted for convenience only and shall not be deemed to
constitute part of this Agreement or to affect the construction thereof.

            Section 16. Definitions. For purposes of this Agreement:

            (a) "Corporate Status" describes the status of a person who is or
was a director, officer, employee, agent or fiduciary of the Company or of any
other direct or indirect subsidiary of the Company.

            (b) "Effective Date" means ___________ __, _____.

            (c) "Expenses" shall be subject to the provisions of Section 7(b)
above and shall include all reasonable attorneys' fees, court costs, transcript
costs and fees of experts. Reasonable Expenses shall not exceed the average for
fees and expenses in the county in which the Expenses have been incurred.

            (d) "Proceeding" includes any action, suit, arbitration, alternate
dispute resolution mechanism, investigation, administrative hearing or any other
proceeding whether civil, criminal, administrative or investigative, whether or
not initiated prior to the Effective Date, except a proceeding initiated by an
Indemnitee pursuant to Section 9 of this Agreement to enforce his or her rights
under this Agreement.

            Section 17. Modification and Waiver. No supplement, modification 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.

            Section 18. Notice by Indemnitee. Indemnitee agrees promptly to
notify the Company in writing upon being served with any summons, citation,
subpoena, complaint, indictment, information or other document relating to any
Proceeding or matter which may be subject to indemnification of Expenses covered
hereunder.

            Section 19. 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: the address of the Indemnitee appearing on
the signature page hereof; and


                                       6
<PAGE>
            (b) If to the Company, to: Stratagene Corporation, Attention:
General Counsel, 11011 North Torrey Pines Road, San Diego, California 92037;

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

            Section 20. Governing Law. The parties agree that this Agreement
shall be governed by, and construed and enforced in accordance with, the laws of
the State of Delaware.

            Section 21. Miscellaneous. Use of the masculine pronoun shall be
deemed to include usage of the feminine pronoun where appropriate.




                  [REMAINDER OF PAGE INTENTIONALLY LEFT BLANK]



                                       7
<PAGE>
            IN WITNESS WHEREOF, the parties hereto have executed this Agreement
on the day and year first above written.

                                       COMPANY:


                                       STRATAGENE CORPORATION


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

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

                                       Title:
                                             -------------------------


                                       INDEMNITEE:



                                       [                   ]
                                        -------------------




                                       ------------------------------







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

                                       ------------------------------

                                       ------------------------------

                                       ------------------------------



                                       8
<PAGE>
            SCHEDULE OF OFFICERS AND DIRECTORS WHO WILL ENTER INTO AN
                           INDEMNIFICATION AGREEMENT

1.    Joseph A. Sorge, M.D.
2.    J. David Tholen
3.    Carlton J. Eibl
4.    Robert Manion
5.    John Reed
6.    Nicolas H. Roelofs, Ph.D.
7.    Ronni L. Sherman
8.    John R. Pouk
9.    Reginald P. Jones