|CERTIFICATION CHIEF
EXECUTIVE OFFICERPURSUANT TO RULE 13a-14(a)



Exhibit 31.1






I, Lance K. Gordon, certify that:
|-----------------------------------------------------------------------------------------------------------------------

|1. | I
have reviewed this quarterly report on Form 10-Q of VaxGen, Inc.
|-- | ------------------------------------------------------------------

|2. | Based
on my knowledge, this report does not contain any untrue statement of a
                    material fact or omit to state a material fact necessary to make the
statements                     made, in light of the circumstances under which such
statements were made, not                     misleading with respect to the period
covered by this report;
|-- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

|3. | Based
on my knowledge, the financial statements, and other financial information
                    included in this report, fairly present in all material respects the
financial                     condition, results of operations and cash flows of the
registrant as of, and                     for, the periods presented in this report;
|-- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

|4. | The
registrants other certifying officer(s) and I are responsible for
                    establishing and maintaining disclosure controls and procedures (as
defined in                     Exchange Act Rules 13a-15(e) and 15d-15(e)) for the
registrant and have:
|-- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

| | (a)
Designed such disclosure controls and procedures, or caused such disclosure
          controls and procedures to be designed under our supervision, to ensure that
          material information relating to the registrant, including its consolidated
          subsidiaries, is made known to us by others within those entities, particularly
          during the period in which this report is being prepared;
| | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

| | (b)
Evaluated the effectiveness of the registrants disclosure controls and
          procedures and presented in this report our conclusions about the effectiveness
          of the disclosure controls and procedures, as of the end of the period covered
          by this report based on such evaluation; and
| | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

| | (c)
Disclosed in this report any change in the registrants internal control
          over financial reporting that occurred during registrants most recent
          fiscal quarter (the registrants fourth quarter in the case of an annual
          report) that has materially affected, or is reasonably likely to materially
          affect, the registrants internal control over financial reporting; and
| | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

|5. | The
registrants other certifying officer(s) and I have disclosed, based on
                    our most recent evaluation of internal control over financial
reporting, to the                     registrants auditors and the audit committee
of registrants board of                     directors (or persons performing the
equivalent functions):
|-- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

| | (a)
            All significant deficiencies and material weaknesses in the design or
operation                of internal control over financial reporting which are
reasonably likely to                adversely affect the registrants ability to
record, process, summarize and                report financial information; and
| | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

| | (b)
Any fraud, whether or not material, that involves management or other employees
          who have a significant role in the registrants internal control over
          financial reporting.
| | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

|August 14, 2003


/s/ Lance K. Gordon
Lance K. Gordon, Chief Executive
Officer
|----------------------------------------------------------------------------------------