RECITALS

                                                                  EXHIBIT 10.12

                     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 XXXXXXX X. XXXXX (the "Executive").

                                    RECITALS

     WHEREAS, the Company and Executive have entered into an Employment
Agreement, dated June 15, 2000 (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
Executive's continued employment with the Company, agree as follows:

                                      TERMS

1.   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.

2.   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.

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

4.   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.

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




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

                                                 NANOGEN, INC.

                                                 By:  /s/ XXXXXX X. XXXXXXXX
                                                    ----------------------------
                                                         Xxxxxx X. Xxxxxxxx
                                                         Chairman and Chief
                                                         Executive Officer


                                                 EXECUTIVE
                                                       /s/ XXXXXXX X. XXXXX
                                                 -------------------------------
                                                         Xxxxxxx X. Xxxxx