**EXHIBIT 31.1**

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**CERTIFICATION**

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I, Michael T. Flavin,****certify that:

 

1.                                       I have reviewed this quarterly**report on Form 10-Q of Advanced Life Sciences Holdings, Inc.;

 

2.                                       Based on my knowledge, thisreport does not contain any untrue statement of a material fact or omit tostate a material fact necessary to make the statements made, in light of thecircumstances under which such statements were made, not misleading withrespect to the period covered by this report;

 

3.                                       Based on my knowledge, thefinancial statements, and other financial information included in this report,fairly present in all material respects the financial condition, results ofoperations and cash flows of the registrant as of, and for, the periodspresented in this report;

 

4.                                       The registrant’sother certifying officer and I are responsible for establishing and maintainingdisclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and15d-15(e)) ****and internal control over financial reporting (asdefined in Exchange Act Rules 13a-15(f) and 15d-15(f))****   for the registrant and have:

 

a)                                      Designed suchdisclosure controls and procedures, orcaused such disclosure controls and procedures to be designed under oursupervision, to ensure that material information relating to the registrant,including its consolidated subsidiaries, is made known to us by others withinthose entities, particularly during the period in which this report is beingprepared;

 

b)                                     Designed such internal controlover financial reporting, or caused such internal control over financialreporting to be designed under our supervision, to provide reasonable assuranceregarding the reliability of financial reporting and the preparation offinancial statements for external purposes in accordance with GAAP;

 

c)                                      Evaluatedthe effectiveness of the registrant’s disclosure controls and procedures andpresented in this report our conclusions about the effectiveness of thedisclosure controls and procedures, as of the end of the period covered by thisreport based on such evaluation; and

 

d)                                     Disclosedin this report any change in the registrant’s internal control over financialreporting that occurred during the registrant’s first fiscal quarter that hasmaterially affected, or is reasonably likely to materially affect, the registrant’sinternal control over financial reporting; and

 

5.                                       Theregistrant’s other certifying officer and I have disclosed, based on our mostrecent evaluation of internal control over financial reporting, to theregistrant’s auditors and the audit committee of the registrant’s board ofdirectors (or persons performing the equivalent functions):

 

a)                                      Allsignificant deficiencies and material weaknesses in the design or operation ofinternal control over financial reporting which are reasonably likely to adverselyaffect the registrant’s ability to record, process, summarize and reportfinancial information; and

 

b)                                     Anyfraud, whether or not material, that involves management or other employees whohave a significant role in the registrant’s internal control over financialreporting.

 

Date: May 12, 2009

 
| /s/ Michael T. Flavin                      |   |
|--------------------------------------------|--------|
| Michael T. Flavin                          |   |
| Chief Executive Officer                    |   |
| Advanced Life Sciences Holdings, Inc. |   |

 

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