Exhibit 31.1 CERTIFICATION OF CHIEF EXECUTIVE OFFICER I, James P. Panek, 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 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)) and
 internal control over financial reporting (as defined in Exchange Act Rules
 13a-15(f) and 15d-15(f)) 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) Designed such internal control over financial
 reporting, or caused such internal control over financial reporting to be
 designed under our supervision, to provide reasonable assurance regarding the
 reliability of financial reporting and the preparation of financial
 statements for external purposes in accordance with generally accepted
 accounting principles;(c) 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(d) 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; and5.
The registrants other certifying officer 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.  October 3, 2007/s/ James P. PanekChief Executive
 Officer 1