EXHIBIT 31.1

MEDICINOVA, INC.

Certification of the Chief Executive Officer and Principal Financial Officer Pursuant to

Section 302 of the Sarbanes-Oxley Act of 2002 for the Period Ended March 31, 2006

I, Yuichi Iwaki, President and
Chief Executive Officer and Acting Chief Financial Officer of MediciNova, Inc., certify that:

1. I have reviewed this
quarterly report on Form 10-Q for the period ended March 31, 2006 of MediciNova, Inc. (the Registrant);

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;

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;

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)) for the Registrant and have:

a) designed such
disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under my supervision, to ensure that material information relating to the Registrant, including its consolidated subsidiaries, is made known to me
by others within those entities, particularly during the period in which this report is being prepared;

b) [omitted
pursuant to SEC Release No. 33-8392];

c) evaluated the effectiveness of the Registrants disclosure controls and
procedures and presented in this report my 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

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

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):

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

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.



Date:

May 10, 2006By:

/s/    YUICHI IWAKIYuichi Iwaki, M.D., Ph.D. and Acting Chief Financial Officer (Principal Executive Officer and Principal Financial Officer)