<Page>

                                                                Exhibit No. 10.7

                            INDEMNIFICATION AGREEMENT

        THIS INDEMNIFICATION AGREEMENT is made effective as of the 1st day of
May, 2002 (the "Agreement"), by and between NANOGEN, INC., a Delaware
corporation (the "Company") and DAVID L. MACDONALD (the "Indemnitee") with
reference to the following facts:

        WHEREAS, the Company desires the benefits of having Indemnitee serve as
an officer and/or director secure in the knowledge that any expenses, liability
and/or losses incurred by him in his good faith service to the Company will be
borne by the Company or its successors and assigns; and

        WHEREAS, Indemnitee is willing to serve in his position with the Company
only on the condition that he be indemnified for such expenses, liability and/or
losses; and

        WHEREAS, the Company and Indemnitee recognize the increasing difficulty
in obtaining liability insurance for directors, officers and agents of a
corporation at reasonable cost; and

        WHEREAS, the Company and Indemnitee recognize that there has been an
increase in litigation against corporate directors, officers and agents; and

        WHEREAS, the Company's Restated Certificate of Incorporation allows and
requires the Company to indemnify its directors, officers and agents to the
maximum extent permitted under Delaware law:

        NOW, THEREFORE, the parties hereby agree as follows:

        1.      DEFINITIONS. For purposes of this Agreement:

        1.1     "Agent" shall mean any person who (a) is or was a director,
officer, employee or agent of the Company or a subsidiary of the Company whether
serving in such capacity or as a director, officer, employee, agent, fiduciary
or other official of another corporation, joint venture, trust or other
enterprise at the request of, for the convenience of, or to represent the
interests of the Company or a subsidiary of the Company or (b) was a director,
officer, employee or agent of Nanogen, Inc., a California corporation and the
predecessor by merger to the Company (the "Predecessor Corporation"), whether
serving in such capacity or as a director, officer, employee, agent, fiduciary
or other official of another corporation, joint venture, trust or other
enterprise at the request of, for the convenience of, or to represent the
interests of such Predecessor Corporation.

        1.2     "Change of Control" shall mean the occurrence of any of the
following events after the date of this Agreement:

<Page>

        (a)     A change in the composition of the board of directors of the
Company (the "Board"), as a result of which fewer than two-thirds of the
incumbent directors are directors who either (a) had been directors of the
Company 24 months prior to such change or (b) were elected, or nominated for
election, to the Board with the affirmative votes of at least a majority of the
directors who had been directors of the Company 24 months prior to such change
and who were still in office at the time of the election or nomination; or

        (b)     Any "person" (as such term is used in sections 13(d) and 14(d)
of the Securities Exchange Act of 1934 (the "Exchange Act"), as amended) through
the acquisition or aggregation of securities is or becomes the beneficial owner,
directly or indirectly, of securities of the Company representing 20 percent or
more of the combined voting power of the Company's then outstanding securities
ordinarily (and apart from rights accruing under special circumstances) having
the right to vote at elections of directors (the "Capital Stock"); PROVIDED,
HOWEVER, that any change in ownership of the Company's securities by any person
resulting solely from a reduction in the aggregate number of outstanding shares
of Capital Stock, and any decrease thereafter in such person's ownership of
securities, shall be disregarded until such person increases in any manner,
directly or indirectly, such person's beneficial ownership of any securities of
the Company.

        1.3     "Disinterested Director" shall mean a director of the Company
who is not and was not a party to the Proceeding in respect of which
indemnification is being sought by Indemnitee.

        1.4     "Expenses" shall be broadly construed and shall include, without
limitation, (a) all direct and indirect costs incurred, paid or accrued, (b) all
attorneys' fees, retainers, court costs, transcripts, fees of experts, witness
fees, travel expenses, food and lodging expenses while traveling, duplicating
costs, printing and binding costs, telephone charges, postage, delivery service,
freight or other transportation fees and expenses, (c) all other disbursements
and out-of-pocket expenses, (d) amounts paid in settlement, to the extent not
prohibited by Delaware Law, and (e) reasonable compensation for time spent by
Indemnitee for which he is otherwise not compensated by the Company or any third
party, actually and reasonably incurred in connection with or arising out of a
Proceeding, including a Proceeding by Indemnitee to establish or enforce a right
to indemnification under this Agreement, applicable law or otherwise.

        1.5     "Independent Counsel" shall mean a law firm or a member of a law
firm that neither is presently nor in the past five years has been retained to
represent: (a) the Company, an affiliate of the Company or Indemnitee in any
matter material to either party or (b) any other party to the Proceeding giving
rise to a claim for indemnification hereunder. Notwithstanding the foregoing,
the term "Independent 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 Company or Indemnitee in an
action to determine Indemnitee's right to indemnification under this Agreement.

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

                                  Page 2 of 11
<Page>

any of the foregoing) actually and reasonably incurred by Indemnitee in
connection with a Proceeding.

        1.7     "Delaware Law" means the Delaware General Corporation Law, as
amended and in effect from time to time, or any successor or other statutes of
Delaware having similar import and effect.

        1.8     "Proceeding" shall mean any pending, threatened or completed
action, hearing, suit or any other proceeding, whether civil, criminal,
arbitrative, administrative, investigative or any alternative dispute resolution
mechanism, including without limitation any such Proceeding brought by or in the
right of the Company.

        2.      EMPLOYMENT RIGHTS AND DUTIES. Subject to any other obligations
imposed on either of the parties by contract or by law, and with the
understanding that this Agreement is not intended to confer employment rights on
either party which they did not possess on the date of its execution, Indemnitee
agrees to serve as a director or officer so long as he is duly appointed or
elected and qualified in accordance with the applicable provisions of the
Restated Certificate of Incorporation (the "Certificate") and Bylaws (the
"Bylaws") of the Company or any subsidiary of the Company and until such time as
he resigns or fails to stand for election or until his employment terminates.
Indemnitee may from time to time also perform other services at the request, or
for the convenience of, or otherwise benefiting the Company. 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 Company shall have no obligation under this Agreement
to continue Indemnitee in any such position.

        2.1     DIRECTORS' AND OFFICERS' INSURANCE.

        (a)     The Company hereby covenants and agrees that, so long as
Indemnitee shall continue to serve as a director or officer of the Company and
thereafter so long as Indemnitee shall be subject to any possible Proceeding,
the Company, subject to Section 2.1(c), shall maintain directors' and officers'
insurance in full force and effect.

        (b)     In all policies of directors' and officers' insurance,
Indemnitee shall be named as an insured in such a manner as to provide
Indemnitee the same rights and benefits, subject to the same limitations, as are
accorded to the Company's directors or officers most favorably insured by such
policy.

        (c)     The Company shall have no obligation to maintain directors' and
officers' insurance if the Company determines in good faith that such insurance
is not reasonably available, the premium costs for such insurance are
disproportionate to the amount of coverage provided, or the coverage provided by
such insurance is limited by exclusions so as to provide an insufficient
benefit.

        3.      INDEMNIFICATION. The Company shall indemnify Indemnitee to the
fullest extent authorized or permitted by Delaware Law and the provisions of the
Certificate and Bylaws of the Company in effect on the date hereof, and as
Delaware Law, the Certificate and Bylaws may

                                  Page 3 of 11
<Page>

from time to time be amended (but, in the case of any such amendment, only to
the extent such amendment permits the Company to provide broader indemnification
rights than Delaware Law, the Certificate and/or Bylaws permitted the Company to
provide before such amendment). The right to indemnification conferred in the
Certificate shall be presumed to have been relied upon by Indemnitee in serving
or continuing to serve the Company as a director or officer and shall be
enforceable as a contract right. Without in any way diminishing the scope of the
indemnification provided by the Certificate and this Section 3, the Company
shall indemnify Indemnitee if and whenever he is or was a witness, party or is
threatened to be made a witness or a party to any Proceeding, by reason of the
fact that he is or was an Agent or by reason of anything done or not done, or
alleged to have been done or not done, by him in such capacity, against all
Expenses and Liabilities actually and reasonably incurred by Indemnitee or on
his behalf in connection with the investigation, defense, settlement or appeal
of such Proceeding. 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 4, 5 and 6 below.

        4.      PAYMENT OF EXPENSES.

        4.1     All Expenses incurred by or on behalf of Indemnitee shall be
advanced by the Company to Indemnitee within 20 days after the receipt by the
Company of a written request for such advance which may be made from time to
time, whether prior to or after final disposition of a Proceeding (unless there
has been a final determination by a court of competent jurisdiction that
Indemnitee is not entitled to be indemnified for such Expenses). Indemnitee's
entitlement to advancement of Expenses shall include those incurred in
connection with any Proceeding by Indemnitee seeking a determination, an
adjudication or an award in arbitration pursuant to this Agreement. The requests
shall reasonably evidence the Expenses incurred by Indemnitee in connection
therewith. Indemnitee hereby undertakes to repay the amounts advanced if it
shall ultimately be determined that Indemnitee is not entitled to be indemnified
pursuant to the terms of this Agreement.

        4.2     Notwithstanding any other provision in this Agreement, to the
extent that Indemnitee has been successful on the merits or otherwise in defense
of any Proceeding, Indemnitee shall be indemnified against all Expenses actually
and reasonably incurred by Indemnitee in connection therewith.

        5.      PROCEDURE FOR DETERMINATION OF ENTITLEMENT TO INDEMNIFICATION.

        5.1     Whenever Indemnitee believes that he is entitled to
indemnification pursuant to this Agreement, Indemnitee shall submit a written
request for indemnification (the "Indemnification Request") to the Company to
the attention of the President with a copy to the Secretary. This request shall
include documentation or information which is necessary for the determination of
entitlement to indemnification and which is reasonably available to Indemnitee.
Determination of Indemnitee's entitlement to indemnification shall be made no
later than 60 days after receipt of the Indemnification Request. The President
or the Secretary shall, promptly upon receipt of Indemnitee's request for
indemnification, advise the Board in writing that Indemnitee has made such
request for indemnification.

                                  Page 4 of 11
<Page>

        5.2     The Indemnification Request shall set forth Indemnitee's
selection of which of the following forums shall determine whether Indemnitee is
entitled to indemnification:

                (1)    A majority vote of Directors who are not parties to the
action with respect to which indemnification is sought, even though less than a
quorum.

                (2)    A written opinion of an Independent Counsel (provided
there are no such Directors as set forth in (1) above or if such Directors as
set forth in (1) above so direct).

                (3)    A majority vote of the stockholders at a meeting at which
a quorum is present, with the shares owned by the person to be indemnified not
being entitled to vote thereon.

                (4)    The court in which the Proceeding is or was pending upon
application by Indemnitee.

        The Company agrees to bear any and all costs and expenses incurred by
Indemnitee or the Company in connection with the determination of Indemnitee's
entitlement to indemnification by any of the above forums.

        6.      PRESUMPTIONS AND EFFECT OF CERTAIN PROCEEDINGS. No initial
finding by the Board, its counsel, Independent Counsel, arbitrators or the
stockholders shall be effective to deprive Indemnitee of the protection of this
indemnity, nor shall a court or other forum to which Indemnitee may apply for
enforcement of this indemnity give any weight to any such adverse finding in
deciding any issue before it. Upon making a request for indemnification,
Indemnitee shall be presumed to be entitled to indemnification under this
Agreement and the Company shall have the burden of proof to overcome that
presumption in reaching any contrary determination. The termination of any
Proceeding by judgment, order, settlement, arbitration award or conviction, or
upon a plea of NOLO CONTENDERE or its equivalent, shall not, of itself, (a)
adversely affect the rights of Indemnitee to indemnification except as
indemnification may be expressly prohibited under this Agreement, (b) create a
presumption that Indemnitee did not act in good faith and in a manner which he
reasonably believed to be in or not opposed to the best interests of the Company
or (c) with respect to any criminal action or proceeding, create a presumption
that Indemnitee had reasonable cause to believe that his conduct was unlawful.

        7.      REMEDIES OF INDEMNITEE IN CASES OF DETERMINATION NOT TO
                INDEMNIFY OR TO ADVANCE EXPENSES.

        7.1     In the event that (a) an initial determination is made that
Indemnitee is not entitled to indemnification, (b) advances for Expenses are not
made when and as required by this Agreement, (c) payment has not been timely
made following a determination of entitlement to indemnification pursuant to
this Agreement or (d) 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 entitlement to such indemnification or advance.
Alternatively, Indemnitee at his option may seek an award in arbitration. If the
parties are unable to agree on an arbitrator, the parties shall provide JAMS
Endispute ("JAMS") with a statement of the nature of the dispute and the desired
qualifications of the arbitrator. JAMS will then provide a list of three

                                  Page 5 of 11
<Page>

available arbitrators. Each party may strike one of the names on the list, and
the remaining person will serve as the arbitrator. If both parties strike the
same person, JAMS will select the arbitrator from the other two names. The
arbitration award shall be made within 90 days following the demand for
arbitration. Except as set forth herein, the provisions of Delaware law shall
apply to any such arbitration. The Company shall not oppose Indemnitee's right
to seek any such adjudication or arbitration award. In any such proceeding or
arbitration Indemnitee shall be presumed to be entitled to indemnification under
this Agreement and the Company shall have the burden of proof to overcome that
presumption.

        7.2     An initial determination, in whole or in part, that Indemnitee
is not entitled to indemnification shall create no presumption in any judicial
proceeding or arbitration that Indemnitee has not met the applicable standard of
conduct for, or is otherwise not entitled to, indemnification.

        7.3     If an initial determination is made or deemed to have been made
pursuant to the terms of this Agreement that Indemnitee is entitled to
indemnification, the Company shall be bound by such determination in the absence
of (a) a misrepresentation of a material fact by Indemnitee in the request for
indemnification or (b) a specific finding (which has become final) by a court of
competent jurisdiction that all or any part of such indemnification is expressly
prohibited by law.

        7.4     The Company and Indemnitee agree herein that a monetary remedy
for breach of this Agreement, at some later date, will be inadequate,
impracticable and difficult of proof, and further agree that such breach would
cause Indemnitee irreparable harm. Accordingly, the Company and Indemnitee agree
that Indemnitee shall be entitled to temporary and permanent injunctive relief
to enforce this Agreement without the necessity of proving actual damages or
irreparable harm. The Company and Indemnitee further agree that Indemnitee shall
be entitled to such injunctive relief, including temporary restraining orders,
preliminary injunctions and permanent injunctions, without the necessity of
posting bond or other undertaking in connection therewith. Any such requirement
of bond or undertaking is hereby waived by the Company, and the Company
acknowledges that in the absence of such a waiver, a bond or undertaking may be
required by the court.

        7.5     The Company shall be precluded from asserting that the
procedures and presumptions of this Agreement are not valid, binding and
enforceable. The Company shall stipulate in any such court or before any such
arbitrator that the Company is bound by all the provisions of this Agreement and
is precluded from making any assertion to the contrary.

        7.6     Expenses incurred by Indemnitee in connection with his request
for indemnification under, seeking enforcement of or to recover damages for
breach of this Agreement shall be borne and advanced by the Company.

        8.      OTHER RIGHTS TO INDEMNIFICATION. Indemnitee's rights of
indemnification and advancement of expenses provided by this Agreement shall not
be deemed exclusive of any other rights to which Indemnitee may now or in the
future be entitled under applicable law, the

                                  Page 6 of 11
<Page>

Certificate, the Bylaws, an employment agreement, a vote of stockholders or
Disinterested Directors, insurance or other financial arrangements or otherwise.

        9.      LIMITATIONS ON INDEMNIFICATION. No indemnification pursuant to
Section 3 shall be paid by the Company nor shall Expenses be advanced pursuant
to Section 3:

        9.1     INSURANCE. To the extent that Indemnitee is reimbursed pursuant
to such insurance as may exist for Indemnitee's benefit. Notwithstanding the
availability of such insurance, Indemnitee also may claim indemnification from
the Company pursuant to this Agreement by assigning to the Company any claims
under such insurance to the extent Indemnitee is paid by the Company. Indemnitee
shall reimburse the Company for any sums he receives as indemnification from
other sources to the extent of any amount paid to him for that purpose by the
Company;

        9.2     SECTION 16(b). On account and to the extent of any wholly or
partially successful claim against Indemnitee for an accounting of profits made
from the purchase or sale by Indemnitee of securities of the Company pursuant to
the provisions of Section 16(b) or the Securities Exchange Act of 1934, as
amended, and amendments thereto or similar provisions of any federal, state or
local statutory law; or

        9.3     INDEMNITEE'S PROCEEDINGS. Except as otherwise provided in this
Agreement, in connection with all or any part of a Proceeding which is initiated
or maintained by or on behalf of Indemnitee, or any Proceeding by Indemnitee
against the Company or its directors, officers, employees or other agents,
unless (a) such indemnification is expressly required to be made by Delaware
Law, (b) the Proceeding was authorized by a majority of the Disinterested
Directors, (c) there has been a Change of Control or (d) such indemnification is
provided by the Company, in its sole discretion, pursuant to the powers vested
in the Company under Delaware Law.

        10.     DURATION AND SCOPE OF AGREEMENT; BINDING EFFECT. This Agreement
shall continue so long as Indemnitee shall be subject to any possible Proceeding
subject to indemnification by reason of the fact that he is or was an Agent and
shall be applicable to Proceedings commenced or continued after execution of
this Agreement, whether arising from acts or omissions occurring before or after
such execution. This Agreement shall be binding upon the Company and its
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 Company) and shall inure to the benefit of Indemnitee and his
spouse, assigns, heirs, devisees, executors, administrators and other legal
representatives.

        11.     NOTICE BY INDEMNITEE AND DEFENSE OF CLAIMS. 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 matter which may be subject to indemnification hereunder,
whether civil, criminal, arbitrative, administrative or investigative;

                                  Page 7 of 11
<Page>

but the omission so to notify the Company will not relieve it from any liability
which it may have to Indemnitee if such omission does not actually prejudice the
Company's rights and, if such omission does prejudice the Company's rights, it
will relieve the Company from liability only to the extent of such prejudice;
nor will such omission relieve the Company from any liability which it may have
to Indemnitee otherwise than under this Agreement. With respect to any
Proceeding:

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

                (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 so to assume the defense thereof and the assumption of such defense,
the Company will not be liable to Indemnitee under this Agreement for any
attorney fees or costs subsequently incurred by Indemnitee in connection with
Indemnitee's defense except as otherwise provided below. Indemnitee shall have
the right to employ his counsel in such Proceeding but the fees and expenses of
such counsel incurred after notice from the Company of its assumption of the
defense thereof and the assumption of such defense shall be at the expense of
Indemnitee unless (i) the employment of counsel by Indemnitee has been
authorized by the Company, (ii) Indemnitee shall have reasonably concluded that
there may be a conflict of interest between the Company and Indemnitee in the
conduct of the defense of such action or that the Company's counsel may not be
adequately representing Indemnitee or (iii) the Company shall not in fact have
employed counsel to assume the defense of such action, in each of which cases
the fees and expenses of counsel shall be at the expense of the Company; 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 not settle any action or
claim which would impose any limitation or penalty on Indemnitee without
Indemnitee's written consent. Neither the Company nor Indemnitee will
unreasonably withhold its or his consent to any proposed settlement.

        11.1    CONTRIBUTION. In order to provide for just and equitable
contribution in circumstances in which the indemnification provided for in this
Agreement is held by a court of competent jurisdiction to be unavailable to
Indemnitee in whole or part, the Company shall, in such an event, after taking
into account, among other things, contributions by other directors and officers
of the Company pursuant to indemnification agreements or otherwise, and, in the
absence of personal enrichment, acts of intentional fraud or dishonesty or
criminal conduct on the part of Indemnitee, contribute to the payment of
Indemnitee's losses to the extent that, after other contributions are taken into
account, such losses exceed: (i) in the case of a director of the Company or any
of its subsidiaries who is not an officer of the Company or any of such
subsidiaries, the amount of fees paid to the director for serving as a director
during the 12 months preceding the commencement of the Proceeding; or (ii) in
the case of a director of the Company or any of its subsidiaries who is also an
officer of the Company or any of such subsidiaries, the amount set forth in
clause (i) plus 5% of the aggregate cash compensation paid to said director for
service in such office(s) during the 12 months preceding the commencement of the
Proceeding; or (iii) in the case of an officer of the Corporation or any of its
subsidiaries, 5% of

                                  Page 8 of 11
<Page>

the aggregate cash compensation paid to such officer for service in such
office(s) during the 12 months preceding the commencement of such Proceeding.

        12.     ESTABLISHMENT OF TRUST. In order to secure the obligations of
the Company to indemnify and to advance Expenses to Indemnitee pursuant to this
Agreement, upon a Change of Control of the Company, the Company or its successor
or assign shall establish a Trust (the "Trust") for the benefit of the
Indemnitee, the trustee (the "Trustee") of which shall be chosen by the Company
and which is reasonably acceptable to the Indemnitee. Thereafter, from time to
time, upon receipt of a written request from Indemnitee, the Company shall fund
the Trust in amounts sufficient to satisfy any and all Liabilities and Expenses
reasonably anticipated at the time of such request for which the Company may
indemnify Indemnitee hereunder. The amount or amounts to be deposited in the
Trust pursuant to the foregoing funding obligation shall be determined by mutual
agreement of the Indemnitee and the Company or, if the Company and the
Indemnitee are unable to reach such an agreement, by Independent Counsel
selected jointly by the Company and the Indemnitee. The terms of the Trust shall
provide that except upon the consent of the Indemnitee and the Company, (i) the
Trust shall not be revoked or the principal thereof invaded, without the written
consent of the Indemnitee, (ii) the Trustee shall advance to the Indemnitee,
within 20 days of a request by the Indemnitee, any and all Expenses, the
Indemnitee hereby agreeing to reimburse the Trustee of the Trust for all
Expenses so advanced if a final determination is made by a court in a final
adjudication from which there is no further right of appeal that the Indemnitee
is not entitled to be indemnified under this Agreement, (iii) the Trust shall
continue to be funded by the Company in accordance with the funding obligations
set forth in this Section, (iv) the Trustee shall promptly pay to the Indemnitee
any amounts to which the Indemnitee shall be entitled pursuant to this
Agreement, and (v) all unexpended funds in the Trust shall revert to the Company
upon a final determination by Independent Counsel selected by Indemnitee or a
court of competent jurisdiction that Indemnitee has been fully indemnified with
respect to the Proceeding giving rise to the funding of the Trust under the
terms of this Agreement. The establishment of the Trust shall not, in any way,
diminish the Company's obligation to indemnify Indemnitee against Expenses and
Liabilities to the full extent required by this Agreement.

        13.     MISCELLANEOUS PROVISIONS.

        13.1    SEVERABILITY; PARTIAL INDEMNITY. If any provision or provisions
of this Agreement (or any portion thereof) shall be held by a court of competent
jurisdiction to be invalid, illegal or unenforceable for any reason whatever:
(a) such provision shall be limited or modified in its application to the
minimum extent necessary to avoid the invalidity, illegality or unenforceability
of such provision; (b) the validity, legality and enforceability of the
remaining provisions of this Agreement shall not in any way be affected or
impaired thereby; and (c) to the fullest extent possible, the provisions of this
Agreement shall be construed so as to give effect to the intent manifested by
the provision (or portion thereof) held invalid, illegal or unenforceable. If
Indemnitee is entitled under any provision of this Agreement to indemnification
by the Company for some or a portion of any Expenses or Liabilities of any type
whatsoever incurred by him in the investigation, defense, settlement or appeal
of a Proceeding but not entitled to all of the total amount thereof, the Company
shall nevertheless indemnify Indemnitee for such total amount

                                  Page 9 of 11
<Page>

except as to the portion thereof for which it has been determined pursuant to
Section 5 hereof that Indemnitee is not entitled.

        13.2    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.

        13.3    INTERPRETATION OF AGREEMENT. It is understood that the parties
hereto intend this Agreement to be interpreted and enforced so as to provide
indemnification to Indemnitee to the fullest extent not now or hereafter
prohibited by law.

        13.4    HEADINGS. The headings of the Sections and 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.

        13.5    PRONOUNS. Use of the masculine pronoun shall be deemed to
include use of the feminine pronoun where appropriate.

        13.6    MODIFICATION AND WAIVER. No supplement, modification or
amendment of this Agreement shall be binding unless executed in writing by both
of the parties to this Agreement. No waiver of any provision of this Agreement
shall be deemed to constitute a waiver of any of the provisions hereof (whether
or not similar) nor shall such waiver constitute a continuing waiver. No waiver
of any provision of this Agreement shall be effective unless executed in
writing.

        13.7    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:

                David L. MacDonald
                Nanogen, Inc.
                10398 Pacific Center Court
                San Diego, California 92121
                Telephone: (858) 410-4600
                Telefax:   (858) 410-4949

                                  Page 10 of 11
<Page>

        (b)     If to the Company to:

                Nanogen, Inc.
                10398 Pacific Center Court
                San Diego, California 92121
                Telephone: (858) 410-4600
                Telefax:   (889) 410-4949
                Attention: Chief Executive Officer

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.

        13.8    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, as applied to contracts between Delaware residents entered
into and to be performed entirely within Delaware.

        13.9    CONSENT TO JURISDICTION. The Company and Indemnitee each hereby
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.

        13.10   ENTIRE AGREEMENT. This Agreement represents the entire agreement
between the parties hereto, and there are no other agreements, contracts or
understanding between the parties hereto with respect to the subject matter of
this Agreement, except as specifically referred to herein or as provided in
Sections 8 and 2.1 hereof.

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

                                            NANOGEN, INC.


                                            By: /s/ V. Randy White
                                                --------------------------------
                                                V. Randy White
                                                Chief Executive Officer

                                            INDEMNITEE

                                            /s/ David L. MacDonald
                                            ------------------------------------
                                                David L. MacDonald
                                                Sr. Vice President of Operations

                                  Page 11 of 11