**Exhibit31.1**

**CERTIFICATION**

I, Deborah Dunsire, certifythat:

1.     I have reviewed this annual report onForm 10-K of Millennium Pharmaceuticals, Inc.;

2.               Based on my knowledge, this report does notcontain any untrue statement of a material fact or omit to state a materialfact necessary to make the statements made, in light of the circumstances underwhich such statements were made, not misleading with respect to the periodcovered by this report;

3.               Based on my knowledge, the financialstatements, and other financial information included in this report, fairlypresent in all material respects the financial condition, results of operationsand cash flows of the registrant as of, and for, the periods presented in thisreport;

4.               The registrant’s other certifying officer andI are responsible for establishing and maintaining disclosure controls andprocedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) andinternal control over financial reporting (as defined in Exchange Act Rules13a-15(f) and 15d-15(f) for the registrant and have:

(a)          Designed such disclosure controls and procedures, or caused suchdisclosure controls and procedures to be designed under our supervision, toensure that material information relating to the registrant, including itsconsolidated subsidiaries, is made known to us by others within those entities,particularly during the period in which this report is being prepared;

(b)         Designed such internal control over financial reporting, or caused suchinternal control over financial reporting to be designed under our supervision,to provide reasonable assurance regarding the reliability of financialreporting and the preparation of financial statements for external purposes inaccordance with generally accepted accounting principles;

(c)          Evaluated the effectiveness of the registrant’s disclosure controls andprocedures and presented in this report our conclusions about the effectivenessof the disclosure controls and procedures, as of the end of the period coveredby this report based on such evaluation; and

(d)         Disclosed in this report any change in the registrant’s internalcontrol over financial reporting that occurred during the registrant’s mostrecent fiscal quarter (the registrant’s fourth fiscal quarter in the case of anannual report) that has materially affected, or is reasonably likely tomaterially affect, the registrant’s internal control over financial reporting;and

5.            The registrant’s other certifying officer andI have disclosed, based on our most recent evaluation of internal control overfinancial reporting, to the registrant’s auditors and the audit committee ofthe registrant’s board of directors (or persons performing the equivalentfunctions):

(a)          All significant deficiencies and material weaknesses in the design oroperation of internal control over financial reporting which are reasonablylikely to adversely affect the registrant’s ability to record, process,summarize and report financial information; and

(b)         Any fraud, whether or not material, that involves management or otheremployees who have a significant role in the registrant’s internal control overfinancial reporting.
| Date: March 1, 2007 | /s/ DEBORAH DUNSIRE                                    |   |
|---------------------|--------------------------------------------------------|--------|
|                | Deborah Dunsire  President and Chief Executive Officer |

 

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