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                                                                 EXHIBIT 10.49


                     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 CLARE BROMLEY, III (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.


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         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/Clare Bromley, III
                                   -----------------------------
                                            Clare Bromley, III