UNITED
STATES


SECURITIES
AND EXCHANGE COMMISSION


WASHINGTON,
D.C. 20549




FORM
10-K/A




(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, 2009.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 000-23357





BIOANALYTICAL
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 AVENUE
                      
                      47906WEST LAFAYETTE, INDIANA
                      
                      (Zip
      code)(Address
      of principal executive offices)





(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





Name of
exchange on which registered:  NASDAQ Capital Market





Indicate
by checkmark if the registrant is a well-known seasoned issuer, as defined by
Rule 405 of the Securities Act.  YES  ̈NO x





Indicate
by checkmark if the registrant is not required to file reports pursuant to
Section 13 or Section 15(d) of the Act.  YES oNO x





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 xNO
 ̈





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. x





Indicate
by check mark whether the registrant is a large accelerated filer, an
accelerated filer, a non-accelerated filer or a smaller reporting
company.  See definitions of “large accelerated filer,” “accelerated
filer,” and “smaller reporting company” in Rule 12b-2 of the Exchange
Act.  (Check one):


Large
accelerated filer  ̈Accelerated
filer  ̈Non-accelerated
filer  ̈Smaller
Reporting Company x





Indicate
by check mark whether the registrant is a shell company (as defined in Rule
12b-2 of the Act).    YES  ̈NO
x





Based on
the closing price on the NASDAQ Global Market on March 31, 2009, the
aggregate market value of the voting and non-voting common equity held by
non-affiliates of the registrant was $4,432,000. As of January 12, 2010,
4,915,318 of registrant's common shares were outstanding. None of the
registrant's Preferred Shares were outstanding as of January 12,
2010.





Documents
Incorporated by Reference





None







TABLE OF
CONTENTS





PageExplanatory
      Note
                1PART
      IIIItem
      10.
                Directors
      and Executive Officers of the Registrant
                2Item
      11.
                Executive
      Compensation
                4Item
      12.
                Security
      Ownership of Certain Beneficial Owners and Management
                11Item
      13.
                Certain
      Relationships and Related Transactions
                12Item
      14.
                Principal
      Accounting Fees and Services
                12PART
      IVItem
      15.
                Exhibits
      and Financial Statement Schedules
                13SIGNATURES
                
                14







EXPLANATORY
NOTE




This Amendment No. 1 on Form 10-K/A
(the “Amendment”) amends the Annual Report on Form 10-K of The Bioanalytical
Systems Inc. Company (“we”, “us”, “our”, or the “Company”) for the fiscal year
ended September 30, 2009, originally filed with the Securities and Exchange
Commission (the “SEC”) on January 13, 2010 (the “Original Filing”). 
Since we did not file our definitive proxy statement within 120 days
of our fiscal year ended September 30, 2009, we are filing this Amendment
to include the information required by Part III, which was omitted from the
Original Filing.  In addition, in connection with the filing of this
Amendment and pursuant to the rules of the SEC, we are including with this
Amendment certain currently dated certifications.  Accordingly, Item 15 of
Part IV has also been amended to reflect the filing of these currently dated
certifications.





This Form 10-K/A does not attempt to
modify or update any other disclosures set forth in the Original Filing, except
as required to reflect the additional information included in Part III of this
Form 10-K/A.  Additionally, this  Form 10-K/A, except for the
additional information included in Part III, speaks as of the filing date of the
Original Filing and does not update or discuss any other Company
developments subsequent to the date of the Original
Filing.


1




PART
III




ITEM 10-DIRECTORS AND EXECUTIVE
OFFICERS OF THE REGISTRANT




The
following information concerns the persons who served as the directors of the
Company as of September 30, 2009, with the additions of David L. Omachinski,
John B. Landis, Ph.D. and A. Charlene Sullivan, Ph.D., who were elected to the
Board on October 8, 2009, November 12, 2009 and January 26, 2010, respectively.
Except as indicated in the following paragraphs, the principal occupations of
these persons have not changed in the past five years. Information concerning
the executive officers of the Company may be found in “Executive Officers of the
Registrant” under Item 1 of our report on Form 10-K filed on January 13, 2010
for fiscal year ending September 30, 2009.




Name
              
              Age
              
              PositionWilliam
      E. Baitinger
              
              76
              
              ChairmanLarry
      S. Boulet
              
              63
              
              DirectorDavid
      W. Crabb
              
              56
              
              DirectorLeslie
      B. Daniels
              
              62
              
              DirectorJohn
      B. Landis, Ph.D.
              
              56
              
              DirectorDavid
      L. Omachinski
              
              57
              
              DirectorRichard
      M. Shepperd
              
              69
              
              Director,
      President and Chief Executive OfficerA.
      Charlene Sullivan, Ph.D.
              
              60
              
              Director





William E. Baitinger has
served as a director of the Company since 1979. Mr. Baitinger was Director of
Technology Transfer for the Purdue Research Foundation from 1988 until 2000. In
this capacity he was responsible for all licensing and commercialization
activities from Purdue University. He currently serves as Special Assistant to
the Vice President for Research at Purdue University. Mr. Baitinger has a
Bachelor of Science degree in Chemistry and Physics from Marietta College and a
Master of Science degree in Chemistry from Purdue University.  Mr.
Baitinger retired from the Board of Directors on January 13, 2010.




Larry S. Boulethas served as
a director of the Company since May 2007. Mr. Boulet was a Senior Audit Partner
with PriceWaterhouseCoopers (PWC), retiring in July 2002, and a National
Financial Services Industry Specialist. For the last five years of his career
with PWC, Mr. Boulet served as Partner-in-charge of the Indianapolis office’s
Private Client Group. Prior to serving on our Board, he served on the Board of
Directors of Century Realty Trust, an Indiana based, real estate investment
trust. He also served as Audit Committee Chairman until the Trust’s sale and
liquidation in 2007. Currently, Mr. Boulet also serves on the Indiana State
University Foundation Board of Directors, where he is the immediate past
Chairman of the Board. He holds a Bachelor of Science degree in Accounting from
Indiana State University.





David W. Crabb, M.D. has
served as a director of the Company since February 2004. He has been Chairman of
the Indiana University Department of Medicine since 2001. Previously he had
served as Chief Resident of Internal Medicine and on the Medicine and
Biochemistry faculty of Indiana University. He was appointed Vice Chairman for
Research for the department and later Assistant Dean for Research. Dr. Crabb
serves on several editorial boards. He is Director of the Indiana Alcohol
Research Center funded by NIAAA. He was a recipient of an NIH Merit Award and
numerous other research and teaching awards. He currently serves on the Board of
Directors of Polymer Technology Sciences, Inc., a privately owned corporation,
and the Board of Trustees of Health and Hospital Corporation of Marion County, a
public agency.





Leslie B. Daniels joined the
BASi Board of Directors in July 2003. Mr. Daniels is a founding partner of CAI,
a private equity fund in New York City, and has served in that capacity for at
least the last five years. He previously was President of Burdge, Daniels &
Co., Inc., a principal in venture capital and buyout investments as well as
trading of private placement securities, and before that, a Senior Vice
President of Blyth, Eastman, Dillon & Co. where he had responsibility for
the corporate fixed income sales and trading departments. Mr. Daniels is a
former Director of Aster-Cephac SA, IVAX Corporation, MIM Corporation, Mylan
Laboratories, Inc., NBS Technologies Inc. and MIST Inc. He was also Chairman of
Zenith Laboratories, Inc. and currently serves as Chairman of Turbo Combustor
Technology Inc. and as a Director of SafeGuard Health Enterprises, Inc. and
Aerosat, Inc.


2


John B. Landis, Ph.D. joined
the BASi Board of Directors in November 2009. Mr. Landis previously served as
Senior Vice President, Pharmaceutical Sciences of Schering-Plough Corporation, a
pharmaceutical company, from September 2003 until his retirement in October
2008.  In that role, Dr. Landis led the global pharmaceutical sciences
function of pharmacy, analytical chemistry, process chemistry, biotechnology,
quality assurance, clinical supplies and devices.  Prior to that, Dr.
Landis served as Senior Vice President, Preclinical Development at Pharmacia
Corporation from 1997 until 2003 and led the global preclinical functions of
toxicology, drug metabolism and pharmacokinetics, pharmaceutical sciences,
analytical chemistry and laboratory animal care.  Dr. Landis also
served as Vice President, Central Nervous System (CNS) Psychiatry, Critical Care
and Inflammation Development for Pharmacia & Upjohn from 1995 through
1997.  Prior to that, Dr. Landis was employed by The Upjohn Company,
where he held positions of increasing responsibility in the areas of analytical
research, quality assurance and quality control. He is a current member of
Purdue University’s Chemistry Leadership Council and Dean’s Leadership Council
for the School of Science and serves on the Advisory Board of South West
Michigan Life Science Venture Capital and NanoMed Scientific and on the board of
directors of Metabolic Solutions Development Company.  Over his
career, Dr. Landis served on several other boards of directors, academic
advisory panels and professional boards.  Dr. Landis earned Ph.D. and
M.S. degrees in Analytical Chemistry from Purdue University and a B.S. degree in
Chemistry from Kent State University.





David L. Omachinski joined the
BASi Board of Directors in October 2009.  Mr. Omaschinski previously
served as Independent Business Consultant and as President and Chief Executive
Officer of Magnum Products, LLC from October 2005 to August 2006. Prior thereto,
he was President and Chief Operating Officer since February 2004, Executive Vice
President, Chief Operating & Financial Officer, and Treasurer since 2002 and
Vice President-Finance, Chief Financial Officer & Treasurer since 1993 of
OshKosh B’Gosh, Inc.  Mr. Omachinksi also serves on the board of
Anchor BanCorp Wisconsin, Inc. since 1999, the University of Wisconsin-Oshkosh
Foundation since 2003, and Chamco, Inc. since 2002.  Mr. Omachinski
received his Bachelor of Business Administration from the University of
Wisconsin-Oshkosh and is a certified public accountant.





Richard M. Shepperd was
elected President and Chief Executive Officer of the Company in September 2006,
and in May 2007, agreed to extend his term until December 2009.  Mr.
Shepperd served for two years prior to joining the Company with Able
Laboratories, Inc., of Cranbury, New Jersey ("Able") as its Chief Restructuring
Officer and Director of Restructuring. Able was formerly a generic
pharmaceutical manufacturing company which filed a voluntary petition for
bankruptcy on July 18, 2005 following the loss of FDA approval for its product
line. Mr. Shepperd's duties for Able included exercising executive authority
over all operational and restructuring activities of Able, which included
advising its Board, creditors committee and courts regarding strategies to
maintain and realize the most value from the company's assets. Able was not
affiliated with the Company. For the two years prior to serving with Able, Mr.
Shepperd served as an independent management consultant for various businesses.
In that capacity, he advised these businesses on developing strategies to
improve their financial health and maximize the assets of those
organizations. On January 27, 2010, Mr. Shepperd retired as President of
the Company and intends to retire as Chief Executive Officer and as a director
of the Company on February 12, 2010.





A. Charlene Sullivan, Ph.D.
has served as a director of the Company since January 26, 2010.  Dr.
Sullivan is an Associate Professor of Management at the School of Management and
the Krannert Graduate School of Management at Purdue University since 1984 and
has been a faculty member at Purdue since 1978.  Throughout her career
at Purdue, Dr. Sullivan has taught undergraduate and graduate classes on
corporate finance, financial institutions and markets and financial and
managerial accounting and has received numerous awards and honors from the
university.  Since 2000 Dr. Sullivan also has served as the Management
Faculty Advisor for the Technical Assistance Program at Purdue, which consults
with small businesses in Indiana.  In addition, Dr. Sullivan has
served as a financial analyst for the Indiana Gaming Commission since 1995 and
as a risk management consultant for Edgar Dunn & Company (a strategy and
consulting firm) since 1994.  Dr. Sullivan has served on the boards of
directors of several private financial institutions and not-for-profit
organizations, including the Federal Reserve Bank of Chicago from 1990 until
1996 and the Purdue Employees Federal Credit Union from 1997 until April
2009.  She currently serves on the board of directors of the Greater
Lafayette Community Foundation and on the Asset-Liability Committee for the
Purdue Employees Federal Credit Union.  Dr. Sullivan earned a B.S.
degree in Home Economics from the University of Kentucky and a M.S. and Ph.D. in
Management from Purdue University.





Audit
Committee




The Board
of Directors has established an Audit Committee. The Audit Committee is
responsible for recommending independent auditors, reviewing, in connection with
the independent auditors, the audit plan, the adequacy of internal controls, the
audit report and management letter and undertaking such other incidental
functions as the board may authorize.  Larry S. Boulet, William E.
Baitinger, David W. Crabb, Leslie B. Daniels and David Omachinski are the
members of the Audit Committee. On January 13, 2010, Mr. Baitinger retired from
the Board of Directors.  The Board of Directors has determined that
each of Mr. Daniels. Mr. Boulet and Mr. Omachinski is an audit committee
financial expert (as defined by Item 401(h) of Regulation S-K). All of the
members of the Audit Committee are “independent” (as defined by Item 7(d)(3)(iv)
of Schedule 14A).


3


Code of
Conduct




The Board
of Directors has adopted a Code of Ethics (as defined by Item 406 of Regulation
S-K) that applies to the Company’s Officers, Directors and employees, a copy of
which is incorporated herein by reference to Exhibit 14 to Form 10-K for the
fiscal year ended September 30, 2006.





Section 16(a) Beneficial
Ownership Reporting Compliance





Section 16(a) of the Securities
Exchange Act of 1934 requires the Corporation’s directors and executive officers
and persons who beneficially own more than ten percent BASi’s Common Shares and
any other person subject to section 16(a) with respect to BASi to file with the
Securities and Exchange Commission reports showing ownership of and changes in
ownership of BASi’s Common Shares and other equity securities. On the basis of
information available to us, we believe that all filing requirements were met
for fiscal 2009.




ITEM
11-EXECUTIVE COMPENSATION





COMPENSATION
DISCUSSION AND ANALYSIS





Compensation Committee and
Compensation Methodology





During the 2009 fiscal year, the
Compensation Committee of the Board was responsible for administering the
compensation and benefit programs for BASi's team members, including the
executive officers. Historically, the Compensation Committee annually reviewed
and evaluated cash compensation and stock option award recommendations along
with the rationale for such recommendations, as well as summary information
regarding the aggregate compensation, provided to BASi's executive officers. The
Compensation Committee examined these recommendations in relation to BASi's
overall objectives and made compensation recommendations to the Board for final
approval. The Compensation Committee also historically sent to the Board for
approval its recommendations on compensation for the Chairman of the Board and
the President and Chief Executive Officer, who do not participate in the
decisions of the Board as to their compensation packages. Neither the Chairman
of the Board nor the President and Chief Executive Officer was a member of the
Compensation Committee during the 2009 fiscal year.





BASi has not hired a compensation
consultant to review its compensation practices. The compensation of BASi's
executives who were employees as of September 30, 2007 was frozen by the
Compensation Committee at the last fiscal year’s compensation level through
fiscal 2009 as part of the effort to return the Company to profitability. Also,
Richard M. Shepperd, Director and CEO negotiated a 43% reduction in his base
salary in January 2009 to further reduce operating costs and provide greater
financial flexibility.





BASi's executive compensation practices
are also affected by the highly competitive nature of the biotechnology industry
and the location of BASi's executive offices in West Lafayette, Indiana. The
fact that West Lafayette, Indiana is a small city in a predominantly rural area
can present challenges to attracting executive talent from other industries and
parts of the country. However, the favorable cost of living in this area and the
small number of competitive employers in this market, enable the Company to pay
generally lower salaries for comparable positions to others in its industry. The
Company has also recruited a number of key employees from Purdue University,
particularly for scientific and technical responsibilities.





The Compensation Committee, in
collaboration with management, is in the process of reviewing the compensation
structure of the Company in order to provide the proper incentives and necessary
retention of key employees, including the named executive officers, to achieve
financial success and an appropriate return to shareholders. These efforts will
be ongoing in the current fiscal year.





The Company intends to develop
compensation packages for BASi's executive officers that meet each of the
following three criteria: (1) market competitive - levels
competitive with companies of similar size and performance to BASi;
(2) performance-based "at risk" pay that is based on both short- and
long-term goals; and (3) shareholder-aligned incentives that are structured
to create alignment between the shareholders and executives with respect to
short- and long-term objectives.


4




Employment Agreements and
Post-Termination Payments





BASi has Employment Agreements with
Messrs. Shepperd, Cox, and Chilton.





Employment Agreement with
Richard M. Shepperd





On May 18, 2007, BASi entered into
an Employment Agreement with Mr. Shepperd to become President and Chief
Executive Officer of BASi. Pursuant to the terms of the agreement between BASi
and Mr. Shepperd, the agreement has an initial twenty-nine month term that
provides for automatic three-month extensions, beginning on January 1,
2010, unless either BASi or Mr. Shepperd gives prior notice of termination.
Mr. Shepperd will also have the opportunity to earn an annual cash bonus at
the discretion of the Board of Directors.





On January 12, 2009, BASi entered into
an Amendment to Employment Agreement with Mr. Shepperd. The Amendment
reduced Mr. Shepperd's base salary from $35,000 per month to $20,000 per month,
which constituted an aggregate reduction of $180,000 through December 31,
2009.  Partially offsetting this, the Amendment provided for a new
housing allowance of $1,000 per month, for a total of $12,000 in calendar
2009.  The Amendment also contemplated that, if a "Change in Control"
(as defined in the employment contract) occurs prior to the end of the term of
the Agreement, Mr. Shepperd will receive a bonus payment of
$201,600.





The agreement provided that
Mr. Shepperd could be entitled to certain severance benefits following
termination of employment. If he is terminated by BASi without "cause," or if
Mr. Shepperd terminates his employment for "good reason," he would be
entitled to the following:




·
            Mr. Shepperd's
      base salary through December 31, 2009, to be paid
      monthly;





·
            All
      vacation accrued as of the date of
termination;





·
            All
      bonus amounts earned but not paid as of the date of termination;
      and





·
            All
      salary earned but not paid through the date of
  termination.





In addition, the non-solicitation
provisions of Mr. Shepperd's employment contract will not apply in the
event of termination without cause or resignation with good reason.





The agreement further provides that if
Mr. Shepperd's employment ends for any reason other than termination
without cause or resignation with “good reason,” Mr. Shepperd shall receive
his earned but unpaid salary through the date of termination, all bonus amounts
earned but not paid as of the date of termination and all vacation accrued
through the date of such termination.





On January 27, 2010, Mr. Shepperd
retired as President of the Company and intends to retire as Chief Executive
Officer and as a director of the Company on February 12, 2010.




Employment Agreement with
Michael R. Cox





On November 6, 2007 BASi entered into
an Employment Agreement with Mr. Cox to serve as Vice President, Finance and
Administration and Chief Financial Officer of BASi. Pursuant to the terms of the
agreement between BASi and Mr. Cox, the agreement has an initial term that ends
on December 30, 2010, but this employment term can be extended for successive
one year periods unless either BASi or Mr. Cox gives the other party written
notice at least 90 days before the end of the term. Mr. Cox will receive a base
salary of $165,000 per year in the first year, which may be increased by the
Company in the future. Mr. Cox is also eligible for any bonus plans adopted by
the Company at the discretion of the Compensation Committee of the Board of
Directors.





The Agreement provides that Mr. Cox
could be entitled to severance benefits following the termination of his
employment, as is further described below under the heading, “Change-in Control
Agreements.” If he is terminated by BASi without "cause", or if Mr. Cox
terminates his employment for "good reason" he would be entitled to the
following:


5





·
            Mr. Cox's base salary, payable
      monthly for 12 months following
  termination;


·
            all vacation accrued as of the
      date of termination;


·
            all bonus amounts earned but not
      paid as of the date of termination;
and


·
            all salary earned but not paid
      through the date of
termination.





In addition, the non-solicitation
provision of Mr. Cox's employment contract will not apply in the event of
termination without cause or resignation with good reason.





Employment Agreement with
Jon Brewer





On October 1, 2008, BASi entered into
an Employment Agreement with Mr. Brewer to serve as Vice President of Sales and
Marketing of BASi. Pursuant to the terms of the agreement between BASi and Mr.
Brewer, the agreement has an initial term that ends on March 31, 2010, but this
employment term can be extended for successive one year periods unless either
BASi or Mr. Brewer gives the other party written notice at least 90 days before
the end of the term. Mr. Brewer will receive a base salary of $155,000 per year
in the first year, which may be increased by the Company in the future.
Additionally, Mr. Brewer received a sign-on bonus in two installments of $5,000
each, on January 1, 2009 and June 1, 2009.  Mr. Brewer will also be
eligible for any bonus plans adopted by the Company at the discretion of the
Compensation Committee of the Board of Directors.





The Agreement provides that Mr. Brewer
could be entitled to severance benefits following the termination of his
employment, as is further described below under the heading, “Change-in Control
Agreements.”  If he is terminated by BASi without "cause", or if Mr.
Brewer terminates his employment for "good reason" he would be entitled to the
following:





·
            Mr. Brewer's base salary, payable
      monthly for 12 months following
  termination;


·
            all vacation accrued as of the
      date of termination;


·
            all bonus amounts earned but not
      paid as of the date of termination;
and


·
            all salary earned but not paid
      through the date of
termination.





In addition, the non-solicitation
provision of Mr. Brewer’s employment contract will not apply in the event of
termination without cause or resignation with good reason.





Mr. Brewer resigned from the Company on
January 4, 2010.





Employment Agreement with
Anthony S. Chilton





On December 1, 2008, BASi entered into
an Employment Agreement with Dr. Chilton to serve as Chief Operating Officer,
Scientific Services of BASi. Pursuant to the terms of the agreement between BASi
and Dr. Chilton, the agreement has an initial term that ends on December 30,
2010, but this employment term can be extended for successive one year periods
unless either BASi or Dr. Chilton gives the other party written notice at least
90 days before the end of the term. Dr. Chilton received a base salary of
$195,000 per year in the first year, which may be increased by the Company in
the future. Additionally, Dr. Chilton received a sign-on bonus in two
installments of $5,000 each, on March 15, 2009 and July 15, 2009.  Dr.
Chilton will also be eligible for any bonus plans adopted by the Company at the
discretion of the Compensation Committee of the Board of Directors.





The Agreement provides that Dr. Chilton
could be entitled to severance benefits following the termination of his
employment, as is further described below under the heading, “Change-in Control
Agreements.” If he is terminated by BASi without "cause", or if Dr. Chilton
terminates his employment for "good reason" he would be entitled to the
following:





·
            Dr. Chilton’s base salary,
      payable monthly for 12 months following
  termination;


·
            all vacation accrued as of the
      date of termination;


·
            all bonus amounts earned but not
      paid as of the date of termination;
and


·
            all salary earned but not paid
      through the date of
termination.





In addition, the non-solicitation
provision of Dr. Chilton’s employment contract will not apply in the event of
termination without cause or resignation with good reason.


6


On January 27, 2010, Dr. Chilton was
elected as the interim President of the Company.





Change-in-Control
Agreements





Mr. Shepperd's Employment Agreement
contains a change-in-control feature. Under Mr. Shepperd's Employment Agreement,
if Mr. Shepperd is “involuntarily terminated” within one year following a
"change in control," Mr. Shepperd will receive $8,333.34 per month for each
month remaining in his employment term. Included in the Amendment to Employment
Agreement entered into by the Company and Mr. Shepperd on January 12, 2009, Mr.
Shepperd also will receive a payment of $201,600.00 in the event of a “change in
control” of the Company, as defined by Article 5 and Addendum A of the May 2007
Agreement.  This amount shall be paid within one (1) month of any such
“change in control” and is intended to be in addition to any Terminal Pay or
other compensation that may become due and owing pursuant to Article 5 of the
May 2007 Agreement.  Mr. Shepperd's ordinary severance compensation
under the Employment Agreement will not apply, and he will be eligible for any
special bonus program.





Mr. Cox's, Mr. Brewer’s and Mr.
Chilton’s Employment Agreements contain a change in control feature. Under these
Employment Agreements, if Mr. Cox, Mr. Brewer or Mr. Chilton are “involuntarily
terminated” for any reason following a change in control, Mr. Cox, Mr. Brewer or
Mr. Chilton would receive an amount equal to their monthly base salary for the
12 months prior to termination payable for at least 2 years. Each would also be
eligible for any special bonus program and be eligible to participate in Company
sponsored benefits, savings and retirement plans, practices, policies and
programs, with the employee contribution paid by the
employee.





“Involuntarily terminated” is
defined in the Employment Agreements as resulting from a “change in control” of
the Company, and due to either (1) the elimination or diminution of the
Employee’s position, authority, duties and responsibilities relative to the
most significant of those held, exercised and assigned at any time during the
six month period immediately preceding a “change in control”; or (2) a change in
location requiring the Employee’s services to be performed at a location other
than the location where the Employee was employed immediately preceding a
“change in control,” other than any office which is the headquarters of the
Company and is less than 35 miles from such location.





A "change in control" is defined in
Messrs. Shepperd’s and Chilton’s Employment Agreements as (1) approval by
shareholders of the Company of (a) any consolidation or merger of the Company in
which the Company is not the continuing or surviving corporation or pursuant to
which shares of stock of the Company would be converted into cash, securities or
other property, other than a consolidation or merger of the Company in which
holders of its common shares immediately prior to the consolidation or merger
have substantially the same proportionate ownership of voting common stock of
the surviving corporation immediately after the consolidation or merger as
immediately before, or (b) a sale, lease, exchange or other transfer (in one
transaction or a series of related transactions) of all or substantially all the
assets of the Company; (2) a change in the majority of members of the Board of
Directors of the Company within a twenty-four (24) month period unless the
election, or nomination for election by the Company shareholders, of each new
director was approved by a vote of two-thirds (2/3) of the directors then still
in office who were in office at the beginning of the twenty-four (24) month
period; or (3) the Company combines with another company and is the surviving
corporation but, immediately after the combination, the shareholders of the
Company immediately prior to the combination do not hold, directly or
indirectly, more than fifty percent (50%) of the share of voting common stock of
the combined company (there being excluded from the number of shares held by
such shareholders, but not from the shares of voting common stock of the
combined company, any shares received by affiliates (as defined in the rules of
the SEC) of such other company in exchange for stock of such other
company).





In addition, Messrs. Cox’s and
Brewer’s Employment Agreements also define a “change in control” to include
either (A) receipt by the Company of a report on schedule 13D, or an amendment
to such a report, filed with the Securities and Exchange Commission (“SEC”)
pursuant to Section 13(d) of the Securities Exchange Act of 1934 (the “1934
Act”) disclosing that any person, group, corporation or other entity is the
beneficial owner, directly or indirectly, of 20% or more of the outstanding
stock of the Company or (B) actual knowledge by the Company of facts, on the
basis of which any person is required to file such a report on schedule 13D, or
an amendment to such a report, with the SEC (or would be required to file such a
report or amendment upon the lapse of the applicable period of time specified in
Section 13(d) of the 1934 Act) disclosing that such a person is the beneficial
owner, directly or indirectly, of 20% or more of the outstanding stock of the
Company.


7


Executive Compensation
Tables





Fiscal 2009 Summary
Compensation Table





The following narrative, tables and
footnotes describe the "total compensation" earned during BASi's 2009 fiscal
year by BASi's NEOs. The total compensation presented below does not reflect the
actual compensation received by BASi's NEOs or the target compensation of BASi's
NEOs during its 2009 fiscal year because there was no value realized by BASi's
NEOs during its 2009 fiscal year from long-term incentives (exercise of
options).  The individual components of the total compensation
calculation reflected in the Summary Compensation Table are broken out
below:





Salary. Base salary earned
during BASi's 2009 fiscal year. The terms of the Employment Agreements governed
the base salary for Messrs. Shepperd, Cox and Chilton.





Bonus. The amounts presented
as bonuses for NEO’s below represent amounts both paid and accrued in regards to
fiscal 2008 and 2009. Annual bonuses were paid in January 2010 for fiscal
2009.




Option Awards. The awards
disclosed under the heading "Option Awards" consist of the aggregate grant date
fair value of the stock option awards granted in fiscal 2009 in accordance with
FASB ASC 718. The grant date fair value of the option awards may vary from the
actual amount ultimately realized by the NEO based on a number of factors. The
factors include BASi's actual operating performance, Common Share price
fluctuations, differences from the valuation assumptions used, the restricted
nature of shares acquired under non-qualified stock option grants, the limited
liquidity in the trading of the Company’s shares and the timing of exercise or
applicable vesting.





All Other Compensation. The
amounts included under the All Other Compensation are described in the footnotes
to the table.





SUMMARY COMPENSATION TABLE





Name and principal
                                                        position
                                                      
                                                      Year
                                                      
                                                      Salary ($)
                                                      
                                                      
                                                      Bonus ($)
                                                      
                                                      
                                                      Option
                                                        Awards (1)
                                                        ($)
                                                      
                                                      
                                                      Company
                                                        Contributions
                                                        to 401(k)($)
                                                      
                                                      
                                                      All Other
                                                        Compensation
                                                        ($)
                                                      
                                                      
                                                      Total ($)Richard
      M. Shepperd,President
      & ChiefExecutive
      Officer;
                                                      
                                                      2008
                                                      
                                                      
                                                      420,000
                                                      
                                                      
                                                      
                                                      —
                                                      
                                                      
                                                      
                                                      —
                                                      
                                                      
                                                      
                                                      5,125
                                                      
                                                      
                                                      
                                                      —
                                                      
                                                      
                                                      
                                                      425,515Director
                                                      
                                                      2009
                                                      
                                                      
                                                      285,000
                                                      (2)
                                                      
                                                      
                                                      —
                                                      
                                                      
                                                      
                                                      —
                                                      
                                                      
                                                      
                                                      3,010
                                                      
                                                      
                                                      
                                                      9,000
                                                      (3)
                                                      
                                                      
                                                      297,010Michael
      R. Cox, VicePresident,
      Finance and
                                                      
                                                      2008
                                                      
                                                      
                                                      165,000
                                                      
                                                      
                                                      
                                                      25,000
                                                      
                                                      
                                                      
                                                      135,600
                                                      (5)
                                                      
                                                      
                                                      2,050
                                                      
                                                      
                                                      
                                                      —
                                                      
                                                      
                                                      
                                                      327,650Chief
      Financial Officer (4)
                                                      
                                                      2009
                                                      
                                                      
                                                      165,000
                                                      
                                                      
                                                      
                                                      —
                                                      
                                                      
                                                      
                                                      —
                                                      
                                                      
                                                      
                                                      1,900
                                                      
                                                      
                                                      
                                                      —
                                                      
                                                      
                                                      
                                                      166,900Anthony
      S. Chilton,Ph.D.,
      Chief Operating
                                                      
                                                      2008
                                                      
                                                      
                                                      —
                                                      
                                                      
                                                      
                                                      —
                                                      
                                                      
                                                      
                                                      —
                                                      
                                                      
                                                      
                                                      —
                                                      
                                                      
                                                      
                                                      —
                                                      
                                                      
                                                      
                                                      —Officer,
      Scientific Services (6)
                                                      
                                                      2009
                                                      
                                                      
                                                      195,000
                                                      
                                                      
                                                      
                                                      10,000
                                                      (7)
                                                      
                                                      
                                                      79,200
                                                      (8)
                                                      
                                                      
                                                      —
                                                      
                                                      
                                                      
                                                      —
                                                      
                                                      
                                                      
                                                      284,200





(1)  Aggregate
grant date fair value of the stock option awards granted in fiscal 2009 in
accordance with FASB ASC 718.  There was only one stock option grant
to an NEO in each of fiscal 2008 and 2009.


(2)  Per
amendment to the employment agreement executed on January 12, 2009, as discussed
above, Mr. Shepperd’s base salary was reduced to $20,000 per month.


(3)  Housing
allowance of $1,000 per month per amendment to the employment agreement executed
on January 12, 2009, as discussed above.


(4)  Effective
October 4, 2007, Mr. Cox also assumed the responsibilities of Chief
Administrative Officer. In November, 2007, as discussed above, Mr. Cox entered
into a new employment agreement and was awarded additional stock option
grants.


(5)  Grant
date fair value of new grant on November 6, 2007 for 30,000 options on common
shares, vesting evenly beginning November 5, 2008 and each successive year
through November 5, 2010.  As of January 29, 2010, 20,000 option
shares have vested and are exercisable.


(6)  Dr.
Chilton was hired on December 1, 2008, during fiscal 2009.


(7)  Sign-on
bonus in two installments of $5,000 each, paid on March 15, 2009 and July 15,
2009.


8


(8)  Grant
date fair value of new grant on December 1, 2008 for 30,000 options on common
shares, vesting evenly beginning December 1, 2009 and each successive year
through December 1, 2011.  As of January 29, 2010, 10,000 option
shares have vested and are exercisable.
 
 Outstanding Equity Awards at
Fiscal Year-End Table
 
 BASi has awarded stock options to
members of its senior management and other BASi team members. The terms of these
awards typically provide for vesting over a defined period of time. Option
awards generally have a four-part vesting schedule in which the first of the
four installments vests on the second anniversary of the grant date. Each
subsequent one-fourth installment thereafter vests on the anniversary of the
grant date for the next three years: however, the Compensation Committee and the
Board has to ability to alter, and occasionally does alter, the vesting schedule
to meet specific objectives, such as the matching of the period of Mr.
Shepperd’s option grant in the current fiscal year to match the period of his
employment contract. The options expire if not exercised within ten years from
the date of grant.
 
 The following table shows the equity
awards granted to BASi's NEOs that were outstanding as of the end of BASi's 2009
fiscal year.
 
 OUTSTANDING
EQUITY AWARDS AT FISCAL 2009YEAR-END
 OPTION
AWARDS
 Number of Securities Underlying
                          Unexercised OptionsName
                        
                        (#)
                          Exercisable
                        
                        
                        (#)
                          Unexercisable
                        
                        
                        Option Exercise
                          Price ($)
                        
                        Option Expiration DateRichard
      M. Shepperd
                        
                        
                        175,000
                        
                        
                        
                        100,000
                        (1)
                        
                        
                        7.10
                        
                        May
      17, 2017Michael
      R. Cox
                        
                        
                        50,000
                          10,000
                        
                        
                        
                        —
                          20,000
                        (2)
                        
                        
                        4.58
                          8.60
                        
                        March
      31, 2014
                          November
      5, 2017Anthony
      S. Chilton, Ph.D.
                        
                        
                        —
                        
                        
                        
                        30,000
                        (3)
                        
                        
                        3.53
                        
                        November
      30,
2018
  (1)
              Options on 100,000 shares vested
      on December 1, 2009.
 (2)
              Options
      on 10,000 shares vested on November 5, 2009 and 10,000 shares vest on
      November 5, 2010.
 (3)
              Options on 10,000 shares vested
      on December 1, 2009, 10,000 shares vest on December 1, 2010 and 10,000
      shares vest on December 1,
2011.
  Fiscal 2009 Option
Exercises
 
 There were no options exercised by
NEO’s in fiscal 2009.
  COMPENSATION
OF DIRECTORS
  BASi's compensation package for
non-employee directors is generally comprised of cash (annual retainers and
committee meeting fees) and stock option awards. The annual pay package is
designed to attract and retain highly-qualified, independent professionals to
represent BASi's shareholders and reflect BASi's position in the industry. With
the 2008 Stock Option Plan, BASi intended to better align director and
shareholder interests through the use of stock option awards to directors.
Actual annual pay varies among directors based on Board committee memberships,
committee chair responsibilities and meetings attended. BASi has not adopted
guidelines with respect to non-employee director ownership of common shares.
Directors who are employees, if any, receive no additional compensation for
their service on the Board.
  [Remainder
of page intentionally left blank.]
  9
  Compensation for non-employee directors
during the 2009 fiscal year consisted of the following:
  Type of Compensation
                      
                      Amount ($)Annual
      retainer for Board membership
                      
                      
                      3,300Annual
      retainer for director serving as Chair of the Audit
    Committee
                      
                      
                      2,000Annual
      retainer for director serving as Chair of the Compensation
      Committee
                      
                      
                      1,000Annual
      retainer for director serving as Chair of the Nominating
      Committee
                      
                      
                      500Meeting
      fee for Board meeting, in person
                      
                      
                      1,000Meeting
      fee for Board meeting, by phone
                      
                      
                      500Committee
      meetings, non-Board meeting days, in person
                      
                      
                      500Committee
      meetings, non-Board meeting days, by phone
                      
                      
                      250Daily
      fee for consultation with management
                      
                      
                      1,000
  For meetings of the standing Board
committees held in conjunction with a meeting of the Board, no additional fees
are paid.
 
 Option Awards
 
 The awards disclosed under the heading
"Option Awards" consist of the aggregate grant date fair value of the stock
option awards granted in fiscal 2009 in accordance with FASB ASC
718.   In fiscal 2009, there were no stock options awarded to
non-employee directors.
 
 Business
Expenses
 
 The directors are reimbursed for their
business expenses related to their attendance at BASi meetings, including room,
meals and transportation to and from Board and committee meetings.  Directors are also
encouraged to attend educational programs related to Board issues and corporate
governance, which are reimbursed by the Company.
 
 Non-Employee
Directors' Compensation Table
 
 The following table shows information
regarding the compensation of BASi's non-employee directors for the 2009 fiscal
year.
 
 DIRECTOR COMPENSATION FOR FISCAL 2009Name
                                            
                                            Fees paid in
                                              cash ($)
                                            
                                            
                                            Option
                                              Awards (1)
                                              ($)
                                            
                                            
                                            All Other
                                              Compensation
                                              ($)
                                            
                                            
                                            Total
                                              ($)William
      E. Baitinger (2)
                                            
                                            
                                            4,150
                                            
                                            
                                            
                                            —
                                            
                                            
                                            
                                            —
                                            
                                            
                                            
                                            4,150Larry
      S. Boulet
                                            
                                            
                                            5,650
                                            
                                            
                                            
                                            —
                                            
                                            
                                            
                                            5,459
                                            (3)
                                            
                                            
                                            11,109Dr.
      David W. Crabb
                                            
                                            
                                            4,150
                                            
                                            
                                            
                                            —
                                            
                                            
                                            
                                            —
                                            
                                            
                                            
                                            4,150Leslie
      B. Daniels
                                            
                                            
                                            3,650
                                            
                                            
                                            
                                            —
                                            
                                            
                                            
                                            —
                                            
                                            
                                            
                                            3,650
 
 (1)
              No
      stock option awards were granted to non-employee directors in fiscal
      2009.
 (2)
              Mr.
      Baitinger retired as Chairman of the Board of Directors and as a director
      on January 13, 2010.
 (3)
              Reimbursement
      to Mr. Boulet for attendance at National Association of Corporate
      Directors conference, travel expenses associated with the conference and
      consultation fees for time incurred in special meetings and research
      associated with the 13-D
filings.
  10
  ITEM
12-SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT
  Ownership ofCommon Stock
 
 The following table shows, as of
January 29, 2010, the number of common shares owned by our directors, executive
officers named in the Summary Compensation Table below, our current directors
and executive officers as a group, and beneficial owners known to us to hold
more than 5% of our outstanding common shares. As of January 29, 2010, there
were 4,915,318 common shares outstanding.
 
 NAME
                      
                      Shares
                        Owned
                      
                      Shares
                        Owned
                        Jointly
                      
                      Shares /
                        Options
                        Owned
                        Beneficially
                      
                      Total
                      
                      %Peter
      T. Kissinger (1)
                      
                      
                      427,747
                      
                      595,910
                      
                      
                      252,310
                      
                      1,275,967
                      
                      
                      26.0Candice
      B. Kissinger (1)
                      
                      
                      250,956
                      
                      595,910
                      
                      
                      429,101
                      
                      1,275,967
                      
                      
                      26.0Thomas
      A. Harenburg (2)
                      
                      
                      276,767
                      
                      —
                      
                      
                      —
                      
                      276,767
                      
                      
                      5.6Larry
      S. Boulet (3)
                      
                      
                      3,500
                      
                      —
                      
                      
                      —
                      
                      3,500
                      
                      
                      *Leslie
      B. Daniels (3)
                      
                      
                      38,042
                      
                      —
                      
                      
                      —
                      
                      38,042
                      
                      
                      *Michael
      R. Cox (3)
                      
                      
                      71,000
                      (4)
                      —
                      
                      
                      —
                      
                      71,000
                      
                      
                      *Richard
      M. Shepperd (3)
                      
                      
                      290,750
                      (5)
                      —
                      
                      
                      —
                      
                      290,750
                      
                      
                      5.9Anthony
      S. Chilton (3)
                      
                      
                      10,000
                      (6)
                      —
                      
                      
                      —
                      
                      10,000
                      
                      
                      *9
      Executive Officers and Directors as a group
                      
                      
                      413,292
                      
                      —
                      
                      
                      —
                      
                      413,292
                      
                      
                      8.4
 
 *
Represents beneficial ownership of less than 1%
 
 (1) Dr.
and Mrs. Kissinger’s shares owned beneficially include the shares owned
individually by the other spouse and 1,354 shares jointly owned with their
children. The address for the Kissingers is 111 Lorene Place, West Lafayette,
Indiana 47906.
 (2) Mr.
Harenburg’s address is 206 N. Main St., Oshkosh,
WI  54901.
 (3)
Addresses are in care of BASi at 2701 Kent Avenue, West Lafayette, Indiana
47906.
 (4)
Shares owned include 70,000 exercisable stock options exercisable within 60 days
of January 29, 2010.
 (5)
Shares owned include 275,000 exercisable stock options exercisable within 60
days of January 29, 2010.
 (6)
Shares owned include 10,000 exercisable stock options exercisable within 60 days
of January 29, 2010.
 
 Equity Compensation Plan
Information
 
 BASi maintains stock option plans that
allow for the granting of options to certain key employees and directors of
BASi. The following table gives information about equity awards under the stock
option plans of BASi:
 
 Plan Category
                        
                        Number of Securitiesto be
                          Issued uponExercise of
                          Outstanding Options
                        
                        
                        Weighted Average
                          Exercise Price of
                          OutstandingOptions
                        
                        
                        Number of SecuritiesRemaining
                          Available forFuture Issuance
                          under theEquity Compensation
                          Plan
                          (Excluding SecuritiesReflected in
                          FirstColumn)Equity
      compensation plans approved by security holders
                        
                        
                        595,000
                        
                        
                        $
                        6.03
                        
                        
                        
                        336,000Equity
      compensation plans not approved by security holders (1)
                        
                        
                        25,000
                        
                        
                        $
                        4.58
                        
                        
                        
                        —Total
                        
                        
                        620,000
                        
                        
                        $
                        5.97
                        
                        
                        
                        336,000
 
 (1)
Includes option to purchase 25,000 shares at $4.58 granted to Michael R. Cox on
April 1, 2004.  This grant is fully vested and expires after 10
years.
  11
  ITEM
13-CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS
  Family
Relationships
 
 There are no family relationships
among the directors and executive officers of BASi.
  Certain Relationships and
Transactions
 
 The Board reviews transactions with
related parties, but has no formal policies in place with respect to such review
or the approval of such transactions.
  ITEM
14-PRINCIPAL ACCOUNTING FEES AND SERVICES
  The Company’s Audit Committee engaged
Crowe Horwath LLP (“Crowe”) as the Company’s independent registered public
accounting firm for the audit of the consolidated financial statements for the
fiscal years ended September 30, 2009, 2008, 2007 (as Crowe Chizek and Company
LLC) and 2006 (as Crowe Chizek and Company LLC).
 
 The Company engaged Crowe as its
principal independent registered public accountants effective as of October 30,
2006. At no time prior to October 30, 2006 had the Company consulted with Crowe
regarding either: (i) the application of accounting principles to a specified
transaction, either completed or proposed; or the type of audit opinion that
might be rendered on the Company’s financial statements; or (ii) any matter that
was either the subject of a disagreement (as that term is defined in Item
304(a)(1)(iv) of Regulation S-K and the related instructions to that Item) or a
reportable event (as that term is defined in Item 304(a)(1)(v) of Regulation
S-K).
 
 Representatives of Crowe are expected
to be present at the Annual Meeting. They will have the opportunity to make a
statement if they desire to do so and will be available to answer appropriate
questions concerning the audit of the Company’s financial
statements.
 
 Fees of Independent
Registered Public Accountants
 
 The aggregate fees billed for the last
two fiscal years for each of the following categories of services are set forth
below:
 
 2009
                  
                  
                  2008Audit
      Fees -Aggregate
      fees for annual audit, quarterly reviews
                  
                  $
                  200,000
                  
                  
                  $
                  240,000Tax
      Fees -Income
      tax services related to compliance with tax laws
                  
                  $
                  120,000
                  
                  
                  $
                  120,000
 
 There were no fees for services other
than the above paid to the Company’s Independent Registered Public
Accountants.
 
 BASi’s policies require that the scope
and cost of all work to be performed for BASi by its independent registered
public accountants must be approved by the Audit Committee. Prior to the
commencement of any work by the independent registered public accountants on
behalf of BASi, the independent registered public accountants provide an
engagement letter describing the scope of the work to be performed and an
estimate of the fees. The Audit Committee and the Chief Financial Officer must
review and approve the engagement letter and the estimate before authorizing the
engagement. All fees were reviewed and approved by the Audit Committee
during fiscal 2009 and 2008. Where fees charged by the independent registered
public accountants exceed the estimate, the Audit Committee must review and
approve the excess fees prior to their payment.
  12
  PART
IV
  ITEM
15-EXHIBITS AND FINANCIAL STATEMENT SCHEDULES
  Documents
filed as a part of this Amendment:
 
 1.
              Exhibits:  The
      following exhibits are filed as part of,or incorporated by reference into,
      this report:
  Number
                    
                    Description of Exhibits(31)
                    31.1
                    Certification
      of Chief Executive Officer (filed herewith).31.2
                    Certification
      of Chief Financial Officer (filed herewith).(32)
                    32.1
                    Written
      Statement of Chief Executive Officer and Chief Financial Officer Pursuant
      to Section 906 of the Sarbanes-Oxley Act of 2002 (18 U.S.C.
      Section 1350) (filed herewith)..
  13
  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.
  BIOANALYTICAL
      SYSTEMS, INC.(Registrant)Date:  
      February 10, 2010
                By:  /s/  Richard M.
      ShepperdRichard
      M. ShepperdChief
      Executive OfficerDate:  February
      10, 2010
                By:  /s/  Michael R.
      CoxMichael
      R. CoxVice
      President, Finance and Administration,Chief
      Financial Officer and
Treasurer
  14