EXHIBIT31.1

CERTIFICATION

I, Kenneth Chahine, certify that:

1.I have reviewed this
Annual Report on Form 10-K of Avigen, 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;   
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| | (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;                
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| | (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                                                                                                          
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| | (d) Disclosed in this report any change in the registrant's
      internal control over financial reporting that occurred during the
      registrant's most recent fiscal quarter (the registrant's fourth fiscal
      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 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 the 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
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| |                                                                                                                                                                                                                                                                                                  
| | (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.                                                                                                     

|Date: March 14, 2008                 
|-------------------------------------
|                                     
|/s/ KENNETHG. CHAHINE                
|Kenneth G. Chahine                   
|Chief Executive Officer and President
|(Principal Executive Officer)        

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