Document:

<PAGE>

                                                                  EXHIBIT 10.10

                     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 HOWARD C. BIRNDORF (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
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.

<PAGE>

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

                                                     NANOGEN, INC.

                                                 By:  /s/ KIERAN GALLAHUE
                                                    --------------------------
                                                        Kieran Gallahue
                                                        President and

                                                 EXECUTIVE
                                                      /s/ HOWARD C. BIRNDORF
                                                  ------------------------------
                                                          Howard C. Birndorf<PAGE>
                                                                  EXHIBIT 10.11

                     FIRST AMENDMENT TO EMPLOYMENT AGREEMENT

     This First Amendment to Employment Agreement ("Amendment"), effective as of
July 28, 2000, except where indicated, is made by and between NANOGEN, INC., a
Delaware corporation (the "Company"), and KIERAN GALLAHUE (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.   TITLE/RESPONSIBILITIES. In Article II TITLE/RESPONSIBILITIES,
          Executive's title, effective as of September 1, 2000, shall be amended
          to "President, Chief Financial Officer and Treasurer," from "Senior
          Vice President, Chief Financial Officer and Treasurer."

     3.   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.

     4.   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.

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

     6.   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

<PAGE>

          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.

     7.   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/ HOWARD C. BIRNDORF
                                                    -------------------------
                                                          Howard C. Birndorf
                                                          Chairman and Chief
                                                          Executive Officer

                                                 EXECUTIVE
                                                      /s/ KIERAN GALLAHUE
                                                  ------------------------------
                                                           Kieran Gallahue<PAGE>

                                                                  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 MICHAEL D. MOORE (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.

<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/ MICHAEL D. MOORE
                                                 -------------------------------
                                                         Michael D. Moore<PAGE>

                                                                 EXHIBIT 10.13

                     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.

Source: [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00017-of-00352.parquet"}, [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00017-of-00352.parquet"}], [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00017-of-00352.parquet"}], [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00017-of-00352.parquet"}]]