**EXHIBIT 31.1**

**CERTIFICATION**

I, Kenneth Chahine, certify that:

| **1.       **I   have reviewed this Annual Report on Form 10-K of Avigen, Inc.;                                                                                                                                                                                                                                                                                  |
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| **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;                                  |
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| **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;                                                     |
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| **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: |
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|                                                                                                                                                                                                                                                                                                                                                                                                | (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 |
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| **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):                              |
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|                                                                                                                                                                                                                                                                                                                                                                                                | (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 10, 2005

| /s/ KENNETH G. CHAHINE                                                                            |   |
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| **Kenneth G. Chahine****Chief   Executive Officer and President   (Principal Executive Officer)** |   |