**Exhibit 31.1**

**CERTIFICATIONS**

I, Jane E. Shaw,certify that:

1.                 I have reviewedthis annual report on Form 10-K/A of Aerogen, Inc.;

2.                 Based on myknowledge, this annual report does not contain any untrue statement of amaterial fact or omit to state a material fact necessary to make the statementsmade, in light of the circumstances in which such statements were made, notmisleading with respect to the period covered by this annual report;

3*.**                *Based on my knowledge, thefinancial statements, and other financial information included in this annualreport, fairly present in all material respects the financial condition,results of operations and cash flows of the registrant as of, and for, theperiods presented in this annual 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-14and 15d-14) for the registrant and have:

(a)          designed such disclosurecontrols and procedures , or caused such disclosure controls and procedures tobe designed under our supervision, to ensure that material information relatingto the registrant, including its consolidated subsidiaries, is made known to usby others within those entities, particularly during the period in which thisannual report is being prepared;

(b)         evaluated theeffectiveness 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

(c)          disclosed in this reportany change in the registrant’s internal control over financial reporting thatoccurred during the registrant’s fourth fiscal quarter that has materially,affected, or is reasonably likely to materially affect, the registrant’sinternal control over financial reporting.;

5.                 The registrant’sother certifying officer and I have disclosed, based on our most recentevaluation of internal control over financial reporting, to the registrant’sauditors and the audit committee of registrant’s board of directors (or personsperforming the equivalent functions):

(a)          all significantdeficiencies and material weaknesses in the design or operation of internalcontrol 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 controls over financialreporting.
| Dated: April 15, 2005 |     |                                    |
|----------------------------|----------|-----------------------------------------|
|                       |     | /s/  JANE E. SHAW, PH.D.      |
| * *                   | * * | Jane E. Shaw,  Ph.D.                    |
| * *                   | * * | *Chairman  and Chief Executive Officer* |
| * *                   | * * | *(Principal  Executive Officer)*        |

 

----