Exhibit 31.1

CERTIFICATION

I, Richard J. Freer, Ph.D., certify that:



| | (1) | I have reviewed this amended Annual Report on Form 10-K of Commonwealth Biotechnologies, 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 referred to in this report, fairly present in all material respects the financial condition, results
of operations and cash flows of the small business issuer as of, and for, the periods presented in this report;
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| | (4) | The small business issuer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)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the small business issuer 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 small business issuer, 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 small business issuer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 small business issuers internal control over financial reporting that occurred during the small business issuers most recent
fiscal annual report that has materially affected, or is reasonably likely to materially affect, the small business issuers internal control over financial reporting; and
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| | (5) | The small business issuers other certifying officer(s) and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the small
business issuers auditors and the audit committee of the small business issuer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
small business issuer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 small business issuers internal control over financial
reporting.
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|                     |  |  |  |                               
|-------------------- |  |  |  | ------------------------------
|Date: March 31, 2009 |  |  |  | /s/    Richard J. Freer, Ph.D.
|                     |  |  |  | Richard J. Freer, Ph.D.       
|                     |  |  |  | Principal Executive Officer