Exhibit 31.1

CERTIFICATION

I, George G. Usher, certify that:

|1. | I have reviewed this quarterly report on Form 10Q of Polydex Pharmaceuticals Limited (the Company) for the fiscal quarter ended April 30, 2009;                                                                                                                                                                            
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|2. | Based on my knowledge, this quarterly 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 Company as of,
and for, the period presented in this report;                                           
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|4. | The Company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 Company and have:
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|5. | The Companys other certifying officer and I have disclosed, based on our most recent evaluation, to the Companys auditors and the audit committee of the Companys board of directors:
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Dated: June 15, 2009

/s/ George G. Usher 
Chief Executive Officer 
Polydex Pharmaceuticals Limited

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