Exhibit 31.1

CERTIFICATION

I, Deborah Dunsire,
certify that:

|1. | I have reviewed this quarterly report on Form 10-Q of Millennium
          Pharmaceuticals, 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.
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|Date: August 4, 2006 | /s/  DEBORAH DUNSIRE                  | 
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|                     |                                       | 
|                     | Deborah Dunsire                       | 
|                     | President and Chief Executive Officer | 
|                     |                                       |