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Employment Agreement [Amendment No. 1] - Nanogen Inc. and James P. O'Connell, Ph.D.

Employment Forms

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                     FIRST AMENDMENT TO EMPLOYMENT AGREEMENT


     This First Amendment to Employment Agreement ("Amendment"), effective as of
July 28, 2000, is made by and between NANOGEN, INC., a Delaware corporation (the
"Company"), and JAMES P. O'CONNELL, PH.D. (the "Executive").

                                    RECITALS

     WHEREAS, the Company and Executive have entered into an Employment
Agreement, dated October 29, 1999 (the "Employment Agreement"); and

     WHEREAS, the Company and Executive wish to amend the Employment Agreement
as described herein.

     NOW, THEREFORE, the Company and Executive, in consideration of the mutual
promises set forth herein, agree as follows:

                                      TERMS

     1. RENEWAL. In Article I, Section B RENEWAL, the last sentence of the
second paragraph shall be amended to decrease the number of months from "18" to
"6", during which the Executive shall be paid his salary and benefits after
termination as described therein.

     2. SECTION 280G. In Article III, Section E SECTION 280G relating to
restrictions on payments made pursuant to the Employment Agreement that may be
considered "excess parachute payments" during Change of Control events as
defined therein, shall be deleted in its entirety.

     3. REMAINDER OF AGREEMENT. The other terms and conditions contained in the
Employment Agreement shall remain in effect pursuant to the Employment Agreement
and such terms and conditions, where applicable, shall also govern this
Amendment.

     4. GOVERNING LAW. This Amendment shall be construed in accordance with the
laws of the State of California, notwithstanding its conflicts of law
provisions.

     5. EXECUTIVE ACKNOWLEDGMENT. Executive acknowledges (a) that he has
consulted with or has had the opportunity to consult with independent counsel of
his own choice concerning this Amendment, and has been advised to do so by the
Company, and (b) that he has read and understands this Amendment, is fully aware
of its legal effect, and has entered into it freely based on his own judgment.

     6. COUNTERPARTS. This Amendment may be executed in one or more
counterparts, all of which taken together constituted one and the same
agreement.

<PAGE>

     Executed by the parties as of the day and year first above written.


                                              NANOGEN, INC.



                                              By: /s/ HOWARD C. BIRNDORF
                                                 -------------------------
                                                 Howard C. Birndorf
                                                 Chairman  and  Chief
                                                 Executive Officer


                                              EXECUTIVE


                                                 /s/ JAMES P. O'CONNELL
                                              -------------------------------
                                              James P. O'Connell, Ph.D.