Exhibit 31.1

CERTIFICATIONS

I, Richard M. Shepperd, Chief Executive Officer, certify that:

| | 1. | I
have reviewed this annual report on Form 10-K of Bioanalytical Systems,      Inc.;
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| | 2. | Based
on my knowledge, this annual 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 annual 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(s) 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)) [clause omitted pursuant to      SEC Release Nos. 33-8238 and
34-47986] 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) | [paragraph
omitted pursuant to SEC Release Nos. 33-8238 and 34-47986];
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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(s) 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:  December 21, 2006 | By:  /s/  Richard M. Shepperd
Richard M. Shepperd
Chief Executive Officer
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