<PAGE>   1
                                                                   EXHIBIT 10.31

                               SECOND AMENDMENT TO
                             BUSINESS LOAN AGREEMENT


         THIS SECOND AMENDMENT TO BUSINESS LOAN AGREEMENT (the "Agreement") is
made as of April 28, 2000, by and between GENOMIC SOLUTIONS INC., a Delaware
corporation ("GSI"), GENOMIC SOLUTIONS, LTD., a United Kingdom corporation
("Genomic UK"), GENOMIC SOLUTIONS, K.K., a Japanese corporation ("Genomic
Japan", and together with GSI and Genomic UK, the "Borrowers"), WHITE PINES
LIMITED PARTNERSHIP I, a Michigan limited partnership "WPLP"), PACIFIC CAPITAL,
L.P., a Delaware limited partnership ("Pacific"), and CHASE VENTURE CAPITAL
ASSOCIATES, a California limited partnership ("Chase", and together with WPLP
and Pacific, the "Requisite Lenders").

                                    RECITALS:

         A. Borrowers and Requisite Lenders are parties to a Business Loan
Agreement dated October 28, 1999, as amended by the First Amendment to Business
Loan Agreement dated as of March 24, 2000 (collectively, the "Loan Agreement"),
pursuant to which, among other things, the Requisite Lenders and certain other
persons (collectively, the "Lenders") advanced to Borrowers the sum of Three
Million Five Hundred Thousand Dollars ($3,500,000"), evidenced by Promissory
Notes delivered by Borrowers to Lenders (collectively, the "Promissory Notes").

         B. GSI wishes to increase its existing line of credit loan with
Comerica Bank (the "Bank") from $22,000,000 to $32,000,000, which amount
constitutes Long-Term Debt under the Loan Agreement and would exceed the amount
of Long-Term Debt which Borrowers may allow to exist under Section 9(a)(ii) of
the Loan Agreement. GSI would like to amend Section 9(a)(ii) of the Loan
Agreement to increase the amount of Long-Term Debt, which it may allow to exist
by an additional $10,000,000.

         C. Under Section 14(i) of the Loan Agreement, the Loan Agreement, any
related document and any other agreement between the parties to the Loan
Agreement, may be modified in a writing executed by Borrowers and Lenders owning
not less than two-thirds of the warrants, or shares of GSI's common stock issued
upon exercise of the warrants, issued pursuant to the Loan Agreement. Requisite
Lenders own more than two-thirds of the warrants, or shares of GSI's common
stock issued upon exercise of the warrants, issued pursuant to the Loan
Agreement.

         D. GSI has filed a registration statement with the SEC for a public
offering and sale of its securities for an aggregate amount in excess of
$50,000,000 (the "IPO") and has applied to have such securities listed on the
Nasdaq National Market System. Borrowers and Requisite Lenders have agreed to
amend the Loan Agreement to allow GSI to increase the amount of Long-Term Debt
which it may allow to exist by and additional $10,000,000 and, if an IPO is
consummated and the securities issued by GSI in the IPO is listed on the Nasdaq
National Market System, to amend the Notes to extend the due date of the Notes
to the first anniversary of the date on which the IPO is consummated, all upon
the terms and conditions set forth in this Amendment.

         NOW, THEREFORE, the parties agree as follows:





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          1. Amendment of Loan Agreement. Section 9(a)(ii) is hereby amended in
     its entirety to read as follows:

                           "(ii) allow consolidated Long-Term Debt to be greater
         than $15,500,000 at any time during 1999, to be greater than
         $46,500,000 at any time during 2000, to be greater than 47,500,000 at
         any time during 2001, to be greater than 51,500,000 at any time during
         2002 or 2003 or to be greater than 48,500,000 as of December 31, 2003
         or at any time thereafter. "Long-Term Debt" shall mean the sum of (x)
         all bank debt, (y) all liabilities classified as long-term in
         accordance with generally accepted accounting principles, and (z) the
         current portion of any liabilities encompassed by "(y)"."

         2. Amendment to Notes. If GSI consummates the IPO and lists its
securities on the Nasdaq National Market System, then, effective as of the date
of the consummation of the IPO, the Notes shall be amended and restated in the
form attached hereto as Exhibit A (the "Amended Notes"). Following the
consummation of the IPO, Lenders shall surrender their Notes to Borrowers in
exchange for the Amended Notes. From and after the date of the consummation of
the IPO and until the Notes are surrendered and exchanged for the Amended Notes,
the Notes shall entitle Lenders only to receive payments of principal, interest,
fees and expenses as provided under the terms of the Amended Notes.

         3. Full Force and Effect. The Loan Agreement, as modified by this
Amendment, remains in full force and effect.

         4. Counterparts and Facsimile Signatures. This Amendment may be
executed in any number of counterparts, each of which shall be deemed to be an
original and all of which together shall constitute one instrument. Copies
(whether facsimile, photostatic or otherwise) of signatures to this Agreement
shall be deemed to be originals and may be relied on to the same extent as the
originals.





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         IN WITNESS WHEREOF, the parties have executed this Amendment on the
date first set forth above.


                                      GENOMIC SOLUTIONS INC.


                                      By: /s/
                                         -----------------------------------
                                         Jeffrey S. Williams, President


                                      GENOMIC SOLUTIONS, LTD.


                                      By: Jeffrey S. Williams
                                         -----------------------------------

                                      Its: Chairman
                                         -----------------------------------

                                      GENOMIC SOLUTIONS, K.K.


                                      By: Jeffrey S. Williams
                                         -----------------------------------
                                      Its: Director
                                         -----------------------------------

                                      WHITE PINES LIMITED PARTNERSHIP I

                                      By: White Pines G.P., L.L.C., its general
                                          partner


                                      By:  /s/
                                         -----------------------------------
                                         Daniel Boyle, Vice President


                                      PACIFIC CAPITAL, L.P.

                                      By: WP Pacific G.P., L.L.C., a general
                                          partner


                                      By:  /s/
                                         -----------------------------------
                                         Daniel Boyle, Vice President



                                      CHASE VENTURE CAPITAL ASSOCIATES


                                      By:  Damion Wicker
                                          -----------------------------------
                                      Its: General Partner
                                          -----------------------------------



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                                    EXHIBIT A

THESE SECURITIES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933 OR
ANY STATE SECURITIES LAWS. THEY MAY NOT BE SOLD OR OFFERED FOR SALE, PLEDGED,
HYPOTHECATED OR OTHERWISE TRANSFERRED IN THE ABSENCE OF AN EFFECTIVE
REGISTRATION STATEMENT AS TO THE SECURITIES UNDER SAID ACT AND ANY APPLICABLE
STATE SECURITIES LAW OR UNLESS THE COMPANY HAS RECEIVED AN OPINION OF COUNSEL
SATISFACTORY TO THE COMPANY THAT SUCH REGISTRATION IS NOT REQUIRED TO EFFECTUATE
SUCH TRANSACTION.

                              AMENDED AND RESTATED
                          P R O M I S S O R Y  N O T E
                          ----------------------------

$                                                     Ann Arbor, Michigan
  ----------                                                    , 2000
                                                      ----------

     FOR VALUE RECEIVED, Genomic Solutions, Inc., a Delaware corporation, 4355
Varsity Drive, Suite E, Ann Arbor, Michigan 48108, Genomic Solutions, Ltd., a
United Kingdom corporation, Unit 3, Forge Close, Little End Road, Eaton Socon,
St. Neots, Cambridgeshire, England PE193TP and Genomic Solutions, K.K., a
Japanese corporation, Gotanda Chuo Bldg. 2F, 3-5, Higashigotanda 2-chome,
Shinagawa-ku, Tokyo 141-0022, Japan, jointly and severally, hereinafter
collectively referred to as "Borrower", promise to pay to the order of _______
_________, hereinafter called the "Lender" or holder, the sum of
_______($______) dollars in lawful money of the United States of America, with
interest at the rate of twelve percent (12.0%) per annum on all sums at any time
unpaid, at ____ _____________ or at such other place as the holder hereof may
designate by written notice to the Borrower, with interest from the date of the
disbursement of the loan, until paid.

     Interest shall be payable quarterly in arrears on each March 31, June 30,
September 30 and December 31, commencing June 30, 2000. On each interest payment
date, (i) 7/12ths of the interest payable on such date shall be paid in cash,
and (ii) 5/12ths of the interest payable on such date shall be paid by the
issuance to Lender of a number of shares of common stock of Parent equal to the
amount of such interest divided by the Minimum Company Value, provided that on
each scheduled interest payment date, Lender may upon ten (10) days, prior
written notice to Parent elect not to receive such payment in shares of common
stock of Parent and instead elect to defer payment of 5/12ths of the interest
due on such scheduled interest payment date, which amount shall then be added to
the outstanding principal balance of this Note with effect as of such payment
date. Interest shall be calculated on a 365 day basis on the unpaid principal
balance for the actual days outstanding. For purposes of the foregoing, "Minimum
Company Value" shall be the same amount determined as the Minimum Company Value
in accordance with the provisions of the Warrants attached to the Loan Agreement
(defined below) as Exhibit B (initially $5.00 per share).
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     The entire unpaid principal balance plus accrued interest and all other
indebtedness shall be due and payable on the earliest of (i) the first
anniversary of this Note, (ii) the date on which (A) Parent's cash and cash
equivalents fall below $50.0 million, or (B) Parent's board of directors
authorizes any action which would cause Parent's cash and cash equivalents to
fall below $50.0 million, (iii) the effective date, immediately after the
effective time, of any merger or consolidation of Parent, (iv) a transfer of
more than 50% of the issued and outstanding common stock of Parent (if
immediately after the transfer the transferee has control of Parent), or (v) a
sale of substantially all of the assets of Parent.

     Until all indebtedness of Borrower to Lender under this Note has been paid
in full, Parent shall furnish to Lender monthly on or before the 5th business
day of each month during the term of this Note a statement setting forth
Parent's cash and cash equivalents as of the last day of the preceding month. If
at any time during the term of this Note Parent's cash and cash equivalents fall
below $52.0 million, then, until such time as Parent's cash and cash equivalents
equal or exceed $52.0 million, Parent shall furnish to Lender by the close of
business on each Wednesday a statement setting forth Parent's cash and cash
equivalents as of the last day of the preceding week.

     This Note, together with the Amended and Restated Promissory Notes of even
date herewith (the "Other Notes") executed and delivered by Borrower to the
other Lenders, as such term is defined in the Loan Agreement (the "April
Lenders"), amends and restates the Promissory Notes dated as of April 23, 1999,
delivered by Borrower to the April Lenders (the "Original Notes"). This Note and
the Other Notes do not constitute the extinguishment of the debt evidenced by
the Original Notes, but represent a renewal of the Original Notes. Any amount
outstanding under the Original Notes, as of the effective date of this Note,
shall constitute an advance under this Note and the Other Notes.

     Parent granted to Lender a security interest in or lien upon all assets of
Parent as described in the Security Agreement and Assignment and Pledge
Agreement dated April 23, 1999 as security for the payment of the Promissory
Note dated April 23, 1999 delivered by the Borrower to the Lender. Such security
interest and lien continue to secure this Note. Borrower may hereafter grant a
security interest in or lien upon other assets as may be described in any other
security agreement, mortgage, or other document executed at any time by the
Borrower and delivered to the Lender (herein collectively termed "Collateral")
as security for the payment of this Note, and for the payment of all other
liabilities, whether direct, indirect, absolute or contingent, now or hereafter
existing, due to become due, several or otherwise, of the Borrower to the Lender
under the Loan Documents (as defined in the Loan Agreement) (herein termed
"Indebtedness").

     Upon an event of default under any security agreement, the Business Loan
Agreement dated April 23, 1999 between Lender, Borrower and others, as amended
by the First Amendment to Business Loan Agreement dated October 28, 1999, the
Second Amendment to Business Loan Agreement dated as of March 24, 2000 and the
Third Amendment to Business Loan Agreement dated April 28, 2000, by and among
the same parties (collectively, the "Loan Agreement"), or any document given in
connection with the Collateral, which event of default is not cured within any

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<PAGE>   6
applicable grace period, (i) this Note and all Indebtedness shall, at the option
of the Lender, become immediately due and payable in full without notice,
presentation or demand for payment, all such being hereby waived by the Borrower
and in such event, it is agreed that the Lender may exercise all rights and
remedies available to it under any security agreement, hypothecation agreement,
Loan Agreement, or other agreement relating to or otherwise securing any of the
Indebtedness or, which may be available to Lender under the Uniform Commercial
Code as in effect in the State of Michigan or other applicable law, and (ii)
this Note shall thereafter bear interest at the rate of sixteen percent (16%)
per annum until such default is cured. Delay or forbearance by the Lender in the
exercise of any right granted hereunder shall not operate as a waiver thereof.

     A late payment fee in the amount of five percent (5.0%) of the installment
due and owing will be assessed against the Borrower in the event the payment
required hereunder is received by the Lender more than ten (10) days after the
due date.

     Provided that all interest payments on this Note shall then be current,
Borrower may prepay this Note in whole at any time or in part from time to time.
This Note is one of various promissory notes executed and delivered by Borrower
pursuant to the Loan Agreement. Borrower shall not prepay this Note in whole or
in part unless Borrower shall concurrently prepay in whole or a prorata part of
all other promissory notes originally executed and delivered by Borrower on the
same date as this Note.

     Notwithstanding any provision to the contrary, it is the intent of the
Lender and Borrower that neither the Lender nor any subsequent holder shall be
entitled to receive, collect, reserve or apply, as interest, any amount in
excess of the maximum lawful rate of interest permitted to be charged by
applicable law or regulations, as amended or enacted from time to time. In the
event the Note calls for an interest payment that exceeds the maximum lawful
rate of interest then applicable, such interest shall not be received,
collected, charged, or reserved until such time as that interest, together with
all other interest then payable, falls within the applicable maximum lawful rate
of interest. In the event the Lender, or any subsequent holder, receives any
such interest in excess of the then maximum lawful rate of interest, such amount
which would be excessive interest shall be deemed a partial prepayment of
principal and treated hereunder as such, or, if the principal indebtedness
evidenced hereby is paid in full, any remaining excess funds shall immediately
be paid to the Borrower.

     Borrower hereby waives presentment, demand, protest and notice of dishonor
and agrees that Borrower shall not be released or discharged by reason of any
release, sale or non-action with respect to the Collateral or other undertakings
securing this Note.

     The security rights of Lender and its assigns shall not be impaired by
Lender's sale, hypothecation, or rehypothecation of any Note of the Borrower or
any item of the Collateral, or by any indulgence, including but not limited to:
(i) any renewal, extension, or modification which Lender may grant with respect
to the Indebtedness or any part thereof, (ii) any surrender, compromise,
release, renewal, extension, exchange, or substitution which Lender may grant in
respect to the Collateral, or (iii) any indulgence granted in respect of any
endorser, co-maker,

                                      -3-
<PAGE>   7
guarantor or surety. The purchaser, assignee, transferee, or pledgee of this
Note, the Collateral, any guarantee, and any other document (or any of them),
sold, assigned, transferred, pledged, or repledged, shall forthwith become
vested with and entitled to exercise all the powers and rights given by this
Note and all Loan Documents of the undersigned to Lender, as if said purchaser,
assignee, transferee, or pledgee were originally named as payee in this Note and
in the Loan Documents.

     This Note shall be construed, interpreted and enforced in accordance with
the laws of the State of Michigan without regard to its conflict of laws
principles. Borrower expressly submits to the jurisdiction and venue in the
Federal or state courts of the State of Michigan by process served by mail on
Borrower at the address set forth above.

     This Note has been negotiated between Borrower and Lender and shall be
deemed to be mutually drafted by them.

     IN WITNESS WHEREOF, this Note has been executed by the duly authorized
officers of the Borrower.

                                   GENOMIC SOLUTIONS INC.


                                   By:
                                      ------------------------------------------
                                           Jeffrey S. Williams, President


                                   GENOMIC SOLUTIONS, LTD


                                   By:
                                      ------------------------------------------

                                   Its:
                                       -----------------------------------------

                                   GENOMIC SOLUTIONS, K.K.


                                   By:
                                      ------------------------------------------

                                   Its:
                                       -----------------------------------------


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