Exhibit 31.1

CERTIFICATION

I, George G. Usher, Chief Executive Officer of Polydex
Pharmaceuticals Limited (the Company) certify that:

|1. | I have reviewed this quarterly report on Form 10Q of the
      Company for the fiscal quarter ended October 31, 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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|   | (a)                                                                                                                                                                                                                                                                                                                                                   
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|   | (b)                                                                                                                                                                                                                                                                                                                                                   
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|   | (c)                                                                                                                                                                                                                                                                                                                                                   
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|   | (d)                                                                                                                                                                                                                                                                                                                                                   
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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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|   | (a)                                                                                                                                                                                                                                                                                                                                                   

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| | (b) | any fraud, whether or not material, that involves
      management or other employees who have a significant role in the Companys
      internal control over financial reporting.

Dated: December 14, 2009

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

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