# UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
WASHINGTON, D.C. 20549

# FORM 10-K/A
(Amendment No. 1)

(Mark One)
[ X ]    ANNUAL  REPORT  PURSUANT TO SECTION 13 OR
15(d)     OF     THE      SECURITIES      EXCHANGE      ACT     OF      1934
            for   the   fiscal   year  ended
September 30, 2003.
OR
[    ]    TRANSITION  REPORT PURSUANT TO
SECTION 13 OR 15(d) OF THE  SECURITIES  EXCHANGE ACT OF 1934
            for the  transition period from 
to.

Commission File Number 000-23357BIOANALYTICAL SYSTEMS, INC.
(Exact name of the registrant as specified in its charter)

|INDIANA                                                        | 35-1345024                          
|-------------------------------------------------------------- | ------------------------------------
|(State or other jurisdiction of incorporation or organization) | (I.R.S. Employer Identification No.)
|2701 KENT AVENUEWEST LAFAYETTE, INDIANA                        | 47906                               
|(Address of principle executive offices)                       | (Zip Code)                          
|(765) 463-4527                                                
|(Registrant's telephone number, including area code)          

Securities     registered     pursuant     to     Section     12(b)    of    the
Act:   None

Securities     registered     pursuant     to     section     12(g)    of    the
Act:   Common Shares

Indicate by check mark whether the registrant (1) has filed all reports required
to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during
the  preceding 12 months (or for such  shorter  period that the  registrant  was
required  to file  such  reports),  and  (2) has  been  subject  to such  filing
requirements for the past 90 days.   YES  
X     
NO

Indicate by check mark if disclosure of delinquent  filers  pursuant to Item 405
of Regulation  S-K is not contained  herein,  and will not be contained,  to the
best of registrant's  knowledge,  in definitive proxy or information  statements
incorporated by reference in Part III of this Form 10-K or any amendment to this
Form
10-K.

Indicate  by check mark  whether  the  registrant  is an  accelerated  filer (as
defined              in              Rule              12b-2).   
YES      
 NO  X

Based on the closing price on the NASDAQ stock market on January 12, 2004,  the
aggregate  market  value of the  voting and  non-voting  common  equity  held by
non-affiliates  of the  registrant  is  $22,979,280.  As of January 12, 2004,
4,869,502 shares of registrants common shares were outstanding.  No shares
of  registrants  Preferred  Stock  were  outstanding  as of  January 12, 2004.

Portions of the following  documents  have been  incorporated  by reference into
this report:

| | Registrant's Document                                                         | Parts Into Which Incorporated
| | ----------------------------------------------------------------------------- | -----------------------------
|
| | Annual Report to security holders for the fiscal yearended September 30, 2003 | Part II                      
|
| | Proxy Statement                                                               | Part III                     

Explanatory Note

The Company is filing this
Amendment No. 1 to Annual Report on Form 10-K/A which was for the fiscal year
ended September 30, 2003, solely to revise the disclosures contained in Item 9A
of Part II of the Form 10-K filed with the Securities and Exchange Commission on
January 13, 2004. Except for the item noted above, no other information is being
amended by this Form 10-K/A. The Company has not updated disclosures in this
Form 10-K/A to reflect any event subsequent to the Company's filing of the
original Form 10-K.

Item 9A.    Controls and Procedures.

Based on their most recent evaluation, which was completed as of September 30,
2003, the Company's Chief Executive Officer and interim Chief Financial Officer
believe that, because of the situation described below, the Company's disclosure
controls and procedures (as defined in Exchange Act Rules 13a-15(e) and
15d-15(e)) were not effective as of September 30, 2003 in timely alerting the
Company's management to material information required to be included in this
Form 10-K and other Exchange Act filings. Upon completing their review, the
Chief Executive Officer and the interim Chief Financial Officer concluded that
the Company was not producing final versions of its Exchange Act reports
sufficiently early to allow the Chief Executive Officer to thoroughly review
them. Since September 30, 2003, the Company has shifted responsibility for the
preparation of the Exchange Act reports to different personnel, has formed a
Disclosure Committee to review its Exchange Act reports, has adopted a more
structured timetable for completing the required disclosure and has obtained
more extensive involvement by the Chief Executive Officer in the preparation of
the reports.

Except as indicated below, there were no significant changes in the Company's
internal controls or other factors that could significantly affect those
controls subsequent to the date of their evaluation, which was completed as of
September 30, 2003.

The Companys independent auditors have informed the audit committee that a
material weakness has been identified in the Company's internal control for the
year ended September 30, 2003. Specifically, the independent auditors noted that
the Company's internal control failed to timely alert management of potential
loan covenant noncompliance. The Company did not have procedures in place to
monitor near-term future financial position and results of operations to enable
it to take operational action in the event of potential loan covenant
noncompliance. The Company has taken measures to correct this material weakness
in the form of enhancing its planning process and creating procedures to more
timely identify credit agreement compliance issues.

The auditors also informed the Company of additional reportable conditions (as
the term reportable conditions is defined by the American Institute
of Certified Public Accountants) that required adjustments to fairly state the
Companys financial statements for the year ended September 30, 2003. These
conditions related to errors in the computation of earned revenues on long-term
contracts at two of the Companys locations, and an error in recognizing
income related to a pre-acquisition contract by one of the Companys
acquired businesses. The Company is in the process of implementing a new system
for managing contracts, that, among other things, applies better controls to
recording and tracking contracts, and automates the computation of earned
revenues. Until this new system is fully functional, additional review
procedures have been established. The Company's controller resigned on July 31,
2003, although she continued to work on a part-time basis through November 4,
2003, and the Chief Financial Officer resigned on October 31, 2003. Since these
resignations, the Company has appointed an interim Chief Financial Officer and
the Company is in the process of recruiting to fill these positions. The Company
has made interim arrangements with a consulting firm to provide the additional
necessary support needed while the search for a new controller and a new Chief
Financial Officer continues.

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# SIGNATURES

Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange
Act of 1934, the Registrant has duly caused this report to be signed on its
behalf by the undersigned, thereunto duly authorized.

|Date:  September 17, 2004 | BIOANALYTICAL SYSTEMS, INC.
  (Registrant)
By:  /s/ Peter T. Kissinger
Peter T. Kissinger
President, Chairman and Chief Executive Officer
By:  /s/ Michael R. Cox
Michael R. Cox
Chief Financial Officer and
VP - Finance
|------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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Pursuant to
the requirements of the Securities Exchange Act of 1934, this report has been
signed below by the following persons on behalf of the Registrant and in the
capacities and on the dates indicated.

|Signature                                | Capacity                                                                                 | Date              
|---------------------------------------- | ---------------------------------------------------------------------------------------- | ------------------
|                                        
|                                        
|/s/ Peter T. KissingerPeter T. Kissinger | President, Chairman and ChiefExecutive Officer and Director(Principal Executive Officer) | September 17, 2004
|                                        
|                                        
|/s/ Michael R. CoxMichael R. Cox         | Chief Financial Officer and VP - Finance(Principal Financial and Accounting Officer)     | September 17, 2004
|                                        
|                                        
|/s/ William E. Baitinger                 | Director                                                                                 | September 17, 2004
|William E. Baitinger                    
|                                        
|                                        
|                                         | Director                                                                                 | September 17, 2004
|Leslie B. Daniels                       
|                                        
|                                        
|                                         | Director                                                                                 | September 17, 2004
|Gayl W. Doster                          
|                                        
|                                        
|/s/ Candice B. Kissinger                 | Director                                                                                 | September 17, 2004
|Candice B. Kissinger                    
|                                        
|                                        
|/s/ Ronald E. Shoup                      | Director                                                                                 | September 17, 2004
|Ronald E. Shoup                         
|                                        
|                                        
|                                         | Director                                                                                 | September 17, 2004
|W. Leigh Thompson                       
|                                        
|                                        

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INDEX TO EXHIBITS

|NumberAssigned InRegulation S-KItem 601 |  | Description of Exhibits
|--------------------------------------- |  | -----------------------

|(31) | 31.1 | Certification of Chief Executive Officer
|---- | ---- | ----------------------------------------

| | 31.2 | Certification of Chief Financial Officer
| | ---- | ----------------------------------------

|(32) |  | Section 1350 Certifications
|---- |  | ---------------------------

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