<PAGE>



    AS FILED WITH THE SECURITIES AND EXCHANGE COMMISSION ON SEPTEMBER 1, 2000

                                                      REGISTRATION NO. 333-94379
================================================================================

                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                             ----------------------


                          PRE-EFFECTIVE AMENDMENT NO. 2
                                       TO
                                    FORM S-3
                             REGISTRATION STATEMENT
                                      UNDER
                           THE SECURITIES ACT OF 1933

                             ----------------------

                             BOSTON BIOMEDICA, INC.
             (Exact Name of Registrant as Specified in Its Charter)

        MASSACHUSETTS                                    04-2652826
(STATE OR OTHER JURISDICTION                               (IRS EMPLOYER
OF INCORPORATION OR ORGANIZATION)                      IDENTIFICATION NUMBER)

                                 375 WEST STREET
                      WEST BRIDGEWATER, MASSACHUSETTS 02379
                                 (508) 580-1900
    (Address, Including Zip Code, and Telephone Number, Including Area Code,
                  of Registrant's Principal Executive Offices)

                       -----------------------------------
                              RICHARD T. SCHUMACHER
                             BOSTON BIOMEDICA, INC.
                                 375 WEST STREET
                           WEST BRIDGEWATER, MA 02379
                                 (508) 580-1900
            (Name, Address, Including Zip Code, and Telephone Number,
                   Including Area Code, of Agent for Service)

                       ----------------------------------
                                   COPIES TO:
                            STEVEN R. LONDON, ESQUIRE
                         BROWN, RUDNICK, FREED & GESMER
                              ONE FINANCIAL CENTER
                           BOSTON, MASSACHUSETTS 02111
                               TEL: (617) 856-8200
                               FAX: (617) 856-8201

                       ----------------------------------

Approximate date of commencement of proposed sale to the public: From time to
time after the effective date of this Registration Statement.

If the only securities being registered on this form are being offered pursuant
to dividend or interest reinvestment plans, please check the following box. [ ]

If any of the securities being registered on this form are to be offered on a
delayed or continuous basis pursuant to Rule 415 under Securities Act of 1933,
other than securities offered only in connection with dividend or interest
reinvestment plans, check the following box. [X]

If this form is filed to register additional securities for an offering pursuant
to Rule 462(b) under the Securities Act, please check the following box and list
the Securities Act registration statement number of the earlier effective
registration statement for the same offering. [ ]

If this form is a post-effective amendment filed pursuant to Rule 462(c) under
the Securities Act, check the following box and list the Securities Act
registration statement number of the earlier effective registration statement
for the same offering. [ ]


If delivery of the prospectus is expected to be made pursuant to Rule 434,
please check the following box.[ ]


     THE REGISTRANT HEREBY AMENDS THIS REGISTRATION STATEMENT ON SUCH DATE OR
DATES AS MAY BE NECESSARY TO DELAY ITS EFFECTIVE DATE UNTIL THE REGISTRANT SHALL
FILE A FURTHER AMENDMENT WHICH SPECIFICALLY STATES THAT THIS REGISTRATION
STATEMENT SHALL THEREAFTER BECOME EFFECTIVE IN ACCORDANCE WITH SECTION 8(a) OF
THE SECURITIES ACT OF 1933 OR UNTIL THE REGISTRATION STATEMENT SHALL BECOME
EFFECTIVE ON SUCH DATE AS THE COMMISSION, ACTING PURSUANT TO SAID SECTION 8(a),
MAY DETERMINE.
<PAGE>

                                              PROSPECTUS (SUBJECT TO COMPLETION)

THE INFORMATION IN THIS PROSPECTUS IS NOT COMPLETE AND MAY BE CHANGED. WE HAVE
FILED A REGISTRATION STATEMENT RELATING TO THE COMMON STOCK WITH THE UNITED
STATES SECURITIES AND EXCHANGE COMMISSION. WE MAY NOT SELL THE COMMON STOCK
UNTIL THE SEC DECLARES THAT THE REGISTRATION STATEMENT IS EFFECTIVE. THIS
PROSPECTUS IS NOT AN OFFER TO SELL THE COMMON STOCK AND IT IS NOT SOLICITING AN
OFFER TO BUY THE COMMON STOCK IN ANY STATE WHERE THE OFFER OR SALE IS NOT
PERMITTED.

                             BOSTON BIOMEDICA, INC.

                      Up to 633,306 Shares of Common Stock


     The shareholders named on page 13 are offering for sale up to 633,306
shares of our common stock under this prospectus.

     Our common stock is traded on the Nasdaq National Market under the symbol
"BBII." On August 31, 2000, the last reported sale price of our common stock was
$4.00 per share.


AN INVESTMENT IN THE COMMON STOCK OFFERED UNDER THIS PROSPECTUS INVOLVES A HIGH
DEGREE OF RISK. SEE "RISK FACTORS" BEGINNING ON PAGE 4.

NEITHER THE SECURITIES AND EXCHANGE COMMISSION NOR ANY STATE SECURITIES
COMMISSION HAS APPROVED OR DISAPPROVED OF THESE SECURITIES OR DETERMINED IF THIS
PROSPECTUS IS TRUTHFUL OR COMPLETE. ANY REPRESENTATION TO THE CONTRARY IS A
CRIMINAL OFFENSE.

                  The date of this prospectus is _______, 2000
<PAGE>

                                TABLE OF CONTENTS


<TABLE>
<S>                                                                  <C>
SUMMARY...............................................................3
RISK FACTORS..........................................................4
WARNINGS REGARDING FORWARD-LOOKING STATEMENTS........................14
USE OF PROCEEDS......................................................14
SELLING SHAREHOLDERS.................................................16
PLAN OF DISTRIBUTION.................................................17
INDEMNIFICATION FOR SECURITIES ACT LIABILITIES.......................19
LEGAL MATTERS........................................................19
EXPERTS..............................................................20
WHERE YOU CAN FIND MORE INFORMATION..................................20
</TABLE>



                                       2
<PAGE>

                                     SUMMARY

                             ABOUT BOSTON BIOMEDICA


         Boston Biomedica provides products and services for the detection and
treatment of infectious diseases such as AIDS, lyme disease, and viral
Hepatitis. We currently operate four business units:


         (1)   BBI Diagnostics, a manufacturer and seller of quality control and
               diagnostic products that increase the accuracy of diagnostic
               tests that are performed IN VITRO, in a test tube or other
               laboratory equipment;


         (2)   BBI Clinical Laboratories, a leading infectious disease testing
               laboratory that specializes in testing blood for the presence or
               absence of nucleic acids in pathogens, testing for tick borne
               diseases and follow-up testing for blood banks after an initial
               test shows questionable or positive results;

         (3)   BBI Biotech Research Laboratories, our research and development
               arm, which provides research and development support for our
               other business units and contract research services and specimen
               storage services for other parties, including various agencies of
               the National Institutes of Health; and,


         (4)   BBI Source Scientific, a manufacturer and seller of laboratory
               and medical instruments.


         In addition, we are conducting research to discover new drugs,
primarily in the AIDS field, from synthetic derivatives of natural plant
compounds. We are also conducting research in a technology that repeatedly
applies and releases pressure on pathogens present in blood or plasma in an
effort to destroy them, with the goal of introducing new solutions for improving
blood plasma safety, for improving specimen preparation in the testing of blood
for the presence or absence of nucleic acids in pathogens and for improving the
treatment of infectious diseases.

         We were organized in Massachusetts in 1978 and commenced significant
operations in 1986. Our principal executive offices are located at 375 West
Street, West Bridgewater, Massachusetts 02379. Our telephone number is (508)
580-1900.



                                       3
<PAGE>

                                  RISK FACTORS


BEFORE YOU BUY SHARES OF OUR COMMON STOCK, YOU SHOULD BE AWARE THAT THERE ARE
VARIOUS RISKS ASSOCIATED WITH THAT PURCHASE, INCLUDING THOSE DESCRIBED BELOW.
YOU SHOULD CONSIDER CAREFULLY THESE RISK FACTORS, TOGETHER WITH ALL OF THE OTHER
INFORMATION IN THIS PROSPECTUS AND THE DOCUMENTS WE HAVE INCORPORATED BY
REFERENCE IN THE SECTION "WHERE YOU CAN FIND MORE INFORMATION" BEFORE YOU DECIDE
TO PURCHASE SHARES OF OUR COMMON STOCK.

WE RELY ON PURCHASE ORDERS AND CONTRACTS FROM A SMALL NUMBER OF CUSTOMERS FOR
A LARGE PORTION OF OUR REVENUES; THE LOSS OF BUSINESS FROM THESE CUSTOMERS
COULD MATERIALLY REDUCE OUR REVENUES AND INCOME.

         Purchase orders account for the majority of our orders; none of our
customers have contractually committed to make future product purchases from us.
In 1999, our three largest customers, Hoffman-La Roche, Inc., Medilabs, Inc. and
Ortho-Diagnostics, Inc. together accounted for approximately 16% of our
revenues. In addition, the various agencies of the National Institutes of
Health, including the National Institutes of Allergies and Infectious Disease,
the National Cancer Institute and the National Heart Lung and Blood Institute,
in the aggregate accounted for approximately 15% of our revenues in 1999. Each
agency within the National Institutes of Health, however, makes independent
purchasing decisions. The loss of any major customer, including any agency
within the National Institutes of Health, or a material reduction in any major
customer's purchases would materially reduce our revenues and our operating
results.

IF WE ARE UNABLE TO INCREASE OUR SALES OF QUALITY CONTROL PRODUCTS TO END-USERS
OF INFECTIOUS DISEASE TEST KITS, THEN OUR FUTURE REVENUES COULD BE LESS THAN WE
HAVE PROJECTED.

         Currently, we sell most of our quality control products for infectious
disease test kits to test kit manufacturers and regulators, which is a
relatively small market. However, we also sell our quality control products to
end-users of infectious disease test kits, including hospital laboratories,
blood donor



                                       4

<PAGE>


testing centers, public health laboratories and commercial laboratories. This
end-user market is a larger market which has not yet become accustomed to using
quality control products to monitor test results, but which we believe is a
growing market. Currently, we expect an increase in both the frequency of use
and the number of products used by our current end-user customers. However,
these end-users of infectious disease test kits may not increase their use of
our products. Further, large manufacturers and distributors of quality control
products that have historically sold to the non-infectious disease market and
that have greater financial, manufacturing and marketing resources than we have
could begin selling their products to the end-users of infectious disease test
kits. If the end-user market for quality control products for infectious disease
testing does not develop further, or if we are unable to increase sales of our
products to this market, our future revenues could be substantially less than we
have projected.

IF OUR BBI SOURCE SCIENTIFIC, INC. AND BBI BIOSEQ, INC. SUBSIDIARIES CONTINUE TO
HAVE SUBSTANTIAL OPERATING LOSSES, THEN WE MAY NOT BE ABLE TO REALIZE THE BOOK
VALUE OF CERTAIN ASSETS.

         As a result of our July 1997 acquisition of Source Scientific, Inc., we
recorded approximately $2,200,000 of goodwill. Since this acquisition, our BBI
Source Scientific subsidiary has incurred cumulative operating losses of
approximately $2,449,000, as of June 30, 2000. That subsidiary may continue to
have operating losses and may never become profitable. As of June 30, 2000, the
net book value of goodwill from the BBI Source Scientific acquisition was
approximately $1,755,000, which represented 6.4% of our total assets on that
date. This amount may become impaired to the extent that expected future
operating profits fall below the current net book value of this goodwill. If BBI
Source Scientific continues to have losses, we may not be able to realize the
net book value of this goodwill.

         Our BBI BioSeq subsidiary has incurred operating losses of
approximately $1,898,000, since its acquisition in September 1998, through June
30, 2000. This subsidiary may not be successful in developing its in-process
technology, and its technology may never achieve commercial viability. If we
cannot successfully commercially develop its technology, our BBI BioSeq
subsidiary may never become profitable.

         Because these subsidiaries have incurred significant operating losses,
we have also reported operating losses in our consolidated results. If we
continue to incur losses on a consolidated basis, we may be unable to realize
some or all of our deferred and current tax assets; and if we determine that
some or all of these tax assets are not realizable we will incur a charge to
earnings and write down the asset to its expected realizable value.



                                       5
<PAGE>


         IF WE ARE UNABLE TO OBTAIN BOTH THE NECESSARY REGULATORY APPROVALS AND
SUBSTANTIAL FUNDS FOR OUR SUBSIDIARIES' PRODUCTS, OUR FUTURE REVENUES AND INCOME
WILL BE LESS THAN WE HAVE PROJECTED.

         Our BBI BioSeq and Panacos Pharmaceuticals subsidiaries are currently
developing products that will require significant additional development,
preclinical and clinical testing regulatory approvals and investment of
substantial funds prior to their commercialization. Our BBI BioSeq subsidiary is
developing laboratory instruments that will use pressure cycling technology, a
technology that repeatedly applies and releases pressure on pathogens present in
blood or plasma in an effort to destroy them. Our BBI Bioseq subsidiary is also
developing its pressure cycling process to refine an existing laboratory
instrument prototype. Both the development of the laboratory instruments and the
pressure cycling process will require substantial capital and development
activities to ready the existing prototype for commercial use. Our Panacos
Pharmaceuticals subsidiary is conducting research relating to compounds,
pharmaceutical compositions, therapeutic methods and vaccine preparations,
primarily in the HIV field, and will require substantial capital to progress to
more advanced stages of drug development, including human clinical trials. The
process of obtaining required regulatory approvals can be costly and
time-consuming, and we may not be able to successfully develop our future
products, prove them to be safe and effective in clinical trials or receive
applicable regulatory approvals. If we are not able to obtain substantial funds,
develop adequate technology and receive regulatory approvals for products being
developed by our BBI BioSeq and Panacos Pharmaceuticals subsidiaries, our future
revenues and income will be less than we have projected.

IF THE FDA REQUIRES CLEARANCE OR APPROVAL FOR CERTAIN OF OUR PRODUCTS AND
INITIATES ENFORCEMENT ACTION FOR OUR FAILURE TO DO SO, WE WILL LIKELY EXPEND
SIGNIFICANT RESOURCES TO RESOLVE THE MATTER.

         In the United States, the Food, Drug, and Cosmetic Act prohibits the
marketing of most IN VITRO diagnostic products until the Food and Drug
Administration either clears or approves the products through processes that are
time-consuming, expensive and uncertain. Some IN VITRO diagnostic products may
be exempt from FDA clearance or approval if they have undergone validation
studies. As of July 31, 2000, 31 of our Accurun 1(R) and Accurun(R) products had
received FDA clearance, and we believe that 17 are exempt from FDA clearance .
During 1999, our Accurun(R) products accounted for approximately 11.55% of our
revenue. Although it has not done so in the past, the FDA may not agree that
some of these products are entitled to an exemption and may adopt a different
interpretation of the Food, Drug, and Cosmetic Act or other laws it administers.
We believe that products which are used only for research and not in diagnostic
procedures are not subject to FDA clearance or approval. We currently label some
of our products "for research use only" because they are not intended for use in
diagnostic procedures, and



                                       6
<PAGE>


have not been cleared or approved by the FDA. It is possible, however, that some
purchasers of these products may use them for diagnostic purposes rather than
for research, despite our labeling. Under any of these circumstances, the FDA
could allege that some or all of these products should have been cleared or
approved, or otherwise validated prior to marketing, and could initiate
enforcement action against us. If the FDA initiates enforcement action against
us, we will likely expend a large amount of time, money, resources and
management attention to resolve the matter. In addition, if we cannot obtain or
are delayed in obtaining FDA clearances or approvals for our products, we may
encounter delays or be unable to ever sell those products.

IF WE FAIL TO COMPLY WITH GOOD MANUFACTURING PRACTICES IN CONNECTION WITH THE
MANUFACTURE OF OUR MEDICAL DEVICE PRODUCTS, WE MAY NOT BE ABLE TO DISTRIBUTE OUR
PRODUCTS AND MAY NOT GENERATE PRODUCT REVENUES.

         We are also subject to strict FDA good manufacturing practice
regulations which govern testing, control and documentation practices, and other
post-marketing restrictions on the manufacture of our medical device products.
Our IN VITRO diagnostic products and our laboratory instrumentation products are
considered "medical device products," as defined by the FDA. Various regulatory
authorities monitor our ongoing compliance with good manufacturing practices and
other applicable regulatory requirements through periodic inspections. If we
fail to comply with good manufacturing practices or other regulatory
requirements, we may not be able to obtain future pre-market clearances or
approvals, or the FDA or other regulatory agencies may impose corrective action
requirements, including total or partial suspension of product distribution,
injunctions, civil penalties, recall or seizure of products, and criminal
prosecution. Any of these events would lead to increased costs and a drain on
resources and could reduce our revenues and operating results.

BECAUSE WE CONDUCT OUR BUSINESS WORLDWIDE, CHANGES IN INTERNATIONAL REGULATORY
REQUIREMENTS MAY MATERIALLY REDUCE OUR TOTAL REVENUES.

         Our international sales accounted for approximately 13.7% of our total
revenues for the year ended December 31, 1999. Several Accurun(R) products are
subject to international regulatory approvals in certain countries (including
Germany and France). These approval processes are similar to the
FDA clearance process. Changes in international regulatory requirements and
policies, including both changes in existing restrictions and future
restrictions on importation of blood and blood derivatives, could result in
reduced international sales, which may materially reduce our total revenues and
income.



                                       7

<PAGE>


IF WE ARE UNABLE TO OBTAIN A STEADY AND ADEQUATE SUPPLY OF RARE SPECIMENS OF
PLASMA AND SERUM, THEN WE MAY BE UNABLE TO PRODUCE SOME OF OUR QUALITY CONTROL
PANEL PRODUCTS AND OUR ACCURUN(R) RUN CONTROLS PRODUCTS.

        We manufacture our diagnostic products, including our quality control
panel products and Accurun(R) run controls products, from human plasma and serum
which we obtain from nonprofit and commercial blood centers in the United States
and from similar sources throughout the world. Our BBI Diagnostics business
unit, which manufactures and sells these diagnostic products, accounts for
approximately 40% of our revenues. Certain of our quality control panel products
and Accurun(R) run control products contain unique and rare plasma specimens
that we collect from individuals who have been infected with particular
diseases. The specimens are unique and rare because we can collect them only
during the brief period of time when the markers for a particular disease in an
infected individual are converting from negative to positive. It is difficult to
identify such infected individuals and to collect specimens from them during the
brief period of time when the markers for a particular disease are converting
from negative to positive. As a result, quantities of these specimens are
limited. As we sell our quality control panel products and run control products,
we must find replacement specimens that are equally unique and rare. We may also
face competition to obtain these specimens which could further limit our ability
to obtain the specimens and to produce certain of our quality control panel
products and run control products. A limit in our ability to produce our
products would reduce our future revenues and operating results.


IF WE ARE NOT ABLE TO REACT QUICKLY TO TECHNOLOGICAL CHANGE, WE MAY NOT BE ABLE
TO COMPETE EFFECTIVELY.


                                       8
<PAGE>

         The infectious disease test kit industry is characterized by rapid and
significant technological change, and changes in customer requirements. As a
result, our ability to continue to compete effectively in this industry depends
upon our ability to enhance our existing products and to develop or acquire, and
introduce in a timely manner, new products that take advantage of technological
advances and respond to customer requirements. We may not be successful in
developing and marketing such new products or enhancements to our existing
products on a timely basis, if at all, and such products may not adequately
address the changing needs of the marketplace. Furthermore, rapid technological
development may result in our products or services becoming obsolete or
noncompetitive before we recover our investment in research, development and
commercialization.


IF WE CANNOT PROTECT OUR INTELLECTUAL PROPERTY, WE MAY BE UNABLE TO COMPETE
EFFECTIVELY.

         Our ability to compete effectively with other companies depends in part
on our ability to maintain the proprietary nature of our technologies and
products. We rely primarily on a combination of trade secrets and non-disclosure
and confidentiality agreements to establish and protect our proprietary rights
in our technology and products. In addition, we have obtained five patents that
we hold jointly with the University of North Carolina at Chapel Hill relating to
compounds, pharmaceutical compositions and therapeutic methods in connection
with our drug discovery program at the University of North Carolina at Chapel
Hill. We also have 15 patents pending related to the pressure cycling technology
that our BBI BioSeq subsidiary is developing. If we have not adequately
protected our technology, or if our competitors misappropriate our intellectual
property, we could lose market share and our future revenues and operating
income could be significantly less than projected.


IF WE ARE UNABLE TO ATTRACT AND RETAIN HIGHLY QUALIFIED SCIENTIFIC AND
MANAGEMENT PERSONNEL, THEN WE MAY NOT BE ABLE TO DEVELOP AND REFINE OUR PRODUCTS
AND SERVICES.

         Our products and services are highly technical and our key personnel
must have specialized training or advanced degrees in order to develop and
refine these products and services. There are a limited number of qualified
scientific and management personnel who possess the technical background
necessary to adequately understand and improve our products and services. We
compete for these personnel with other companies, academic institutions,
government entities and other organizations engaged in research and development
of quality control products. If we are unable to attract and retain scientific
and management personnel with the appropriate credentials who are capable of
developing and


                                       9
<PAGE>

refining our products and services, then our products and services could become
inaccurate or unreliable, or could fail to obtain FDA approval and we may be
unable to deliver new products.


PENDING LITIGATION COULD RESULT IN SUBSTANTIAL COSTS AND MAY DIVERT MANAGEMENT'S
ATTENTION AND RESOURCES.

         On August 18, 2000, we received a summons and complaint from Paradigm
Group, LLC, naming us as a defendant. Paradigm Group, LLC is a selling
shareholder in this registration statement. The suit, filed in the Circuit Court
of Cook County, Illinois, alleges breach of contract claims and fraud against us
in connection with the sale by us to them of warrants to purchase our shares of
common stock, the exercise of those warrants by Paradigm Group, LLC, and a delay
in the registration of those shares in this registration statement. Paradigm
Group, LLC, seeks several remedies, including $3 million in damages or
unspecified monetary damages, return of the $42,500 purchase price for the
warrants and rescission of its exercise of the warrants, and unspecified
punitive damages. We have announced that we intend to vigorously defend this
matter. This lawsuit could result in substantial costs and may divert
management's attention and resources. Any adverse determination in this case
could also subject us to significant liabilities.


INSIDERS CONTROL A SIGNIFICANT PERCENTAGE OF VOTING POWER AND MAY EXERCISE THEIR
VOTING POWER IN A MANNER ADVERSE TO OTHER SHAREHOLDERS' INTERESTS.


         Our chief executive officer, Richard T. Schumacher, his relatives, and
our other existing officers and directors collectively have voting control over
approximately 35% of the outstanding shares of our common stock. Accordingly,
these shareholders, should they choose to act in concert, are in a position to
exercise a significant degree of control and to significantly influence
shareholder votes on the election of directors, increasing the authorized
capital stock, and authorizing mergers and sales of assets. These shareholders
may act in a manner that is adverse to your personal interests.


ANTI-TAKEOVER PROVISIONS IN OUR CHARTER AND BY-LAWS MAY DISCOURAGE THIRD PARTIES
FROM PURSUING A TAKEOVER.

         Our amended and restated articles of organization and restated bylaws
contain provisions that may make an acquisition of us more difficult and
discourage changes in our management. These provisions could limit the price
that investors might be willing to pay in the future for shares of our common
stock. These provisions include:


                                       10
<PAGE>

         -     a classified board of directors;

         -     advance notice to the board of directors of shareholder proposals
               and shareholder nominees for the board of directors;

         -     limitations on the ability of shareholders to remove directors
               and call shareholders meetings;

         -     a provision that allows a majority of the directors to fill
               vacancies on the board of directors; and

         -     the ability of the board of directors to issue, without further
               shareholder approval, preferred stock with rights and privileges
               that could be senior to the common stock.

         We are also subject to the Massachusetts General Laws which, subject to
certain exceptions, prohibit a Massachusetts corporation from engaging in any of
a broad range of business combinations with any "interested shareholder" for a
period of three years following the date that shareholder became an interested
shareholder. These provisions could discourage a third party from pursuing a
takeover at a price considered attractive by many shareholders and could have
the effect of preventing or delaying a potential acquirer from acquiring
control.


                                       11
<PAGE>

                  WARNINGS REGARDING FORWARD-LOOKING STATEMENTS

         Some of the statements contained in this prospectus under "Summary" and
"Risk Factors," and in the documents incorporated by reference, are
forward-looking statements made pursuant to the safe harbor provisions of the
Private Securities Litigation Reform Act of 1995. In essence, forward-looking
statements are predictions of future events. Although we would not make
forward-looking statements unless we believe we have a reasonable basis for
doing so, we cannot guarantee their accuracy, and actual results may differ
materially from those we anticipated due to a number of uncertainties, many of
which we are not aware. We urge you to consider the risks and uncertainties
discussed under "Risk Factors" and in the other documents filed with the SEC
that we have referred you to in evaluating our forward-looking statements.

         You should also understand that we have no plans to update our
forward-looking statements. Our forward-looking statements speak only as of the
date of this prospectus, or in the case of forward-looking statements in
documents incorporated by reference, as of the date of those documents.

     We generally identify forward-looking statements with the words "plan,"
"expect," "anticipate," "believe," "intend," "estimate," "continue," "will,"
"may," "should" and similar expressions. Examples of our forward-looking
statements may include statements related to:

         -     our plans, objectives, expectations and intentions;

         -     the timing, availability, cost of development and functionality
               of products under development or recently introduced; and

         -     the anticipated markets for our products and the success of our
               products in those markets.

                                USE OF PROCEEDS

         The selling shareholders are selling all of the shares covered by this
prospectus for their own account. Accordingly, we will not receive any proceeds
from the resale of the shares.


         However, the 633,306 shares of our common stock that we are registering
under this prospectus include shares that may be issued to selling shareholders
upon the conversion of outstanding stock purchase warrants.



                                       12
<PAGE>


         Paradigm Group, L.L.C. obtained its shares upon the exercise of stock
purchase warrants that it received in connection with its investment in Boston
Biomedica. The total purchase price for the warrants was $50,000. David Kavrell,
Brian Friedman, Craig Gould, Steven Rothstein and Robert Daskal obtained their
shares upon the exercise of stock purchase warrants that they received by
transfer from Paradigm Group. These shareholders and Paradigm Group have agreed
to pay us a total of $2,225,000, as payment of the aggregate exercise price of
their warrants, on the business day after the SEC declares our registration
statement relating to these shares effective.

         National Securities received stock purchase warrants as a fee for
services rendered in connection with Paradigm Group's investment in Boston
Biomedica. National Securities may exercise warrants to purchase up to 40,000
shares of our common stock at an exercise price of $4.25 per share and warrants
to purchase up to 25,000 shares of our common stock at an exercise price of
$8.00 per share in connection with Paradigm Group's exercise of its warrants.
This transaction is the subject of the litigation described under "Risk Factors"
beginning on page 4. In addition, National Securities may exercise warrants to
purchase up to 10,000 shares of our common stock at an exercise price of $5.25
per share. National Securities' warrants expire on August 15, 2001.

         MdBio, Inc., received 29,153 stock units in connection with its award
of $175,000 to Boston Biomedica under a manufacturing incentive program that
MdBio instituted. Each stock unit consists of one share of our common stock and
a warrant to purchase one additional share of our common stock at an exercise
price of $10.00 per share. MdBio's warrants expire on September 29, 2003.

         We will use any proceeds which we will receive from the exercise of
these stock purchase warrants for working capital purposes.


         We prepared this prospectus to satisfy our obligations to the selling
shareholders to register their shares. We will bear the expenses relating to
this registration, other than selling discounts and commissions, which will be
paid by the selling shareholders.


                                       13
<PAGE>

                              SELLING SHAREHOLDERS


         The selling shareholders named below are offering for sale up to
633,306 shares of our common stock under this prospectus. We will not receive
any proceeds from those sales. The 633,306 shares of our common stock that we
are registering under this prospectus include shares that may be issued to
selling shareholders upon the conversion of outstanding stock purchase warrants.

         The following table sets forth information regarding the beneficial
ownership of our common stock by the selling shareholders as of August 31, 2000
and as adjusted to reflect the sale or transfer by the selling shareholders of
the shares of our common stock being registered under this prospectus, including
the sale or transfer of shares of our common stock underlying warrants held by
selling shareholders. This information is based upon information received from
or on behalf of the selling shareholders.

<TABLE>
<CAPTION>
                                                           SHARES BENEFICIALLY       NUMBER OF   SHARES BENEFICIALLY
                                                                  OWNED            SHARES BEING      OWNED AFTER
                                                            PRIOR TO OFFERING        OFFERED          OFFERING
                                                            -----------------      ------------  -------------------
NAME OF SECURITYHOLDER                                      NUMBER     PERCENT        NUMBER      NUMBER   PERCENT
                                                            ------     -------        ------      ------   -------
<S>                                                       <C>           <C>          <C>             <C>      <C>
Paradigm Group, L.L.C.(1)                                 425,000       7.76%        425,000         0        *
David Kavrell                                              15,000           *         15,000         0        *
Brian Friedman                                             10,000           *         10,000         0        *
Craig Gould                                                20,000           *         20,000         0        *
Steven Rothstein                                           20,000           *         20,000         0        *
Robert Daskal                                              10,000           *         10,000         0        *
National Securities                                        75,000 (2)   1.37%         75,000         0        *
MdBio, Inc.                                                58,306 (3)   1.06%         58,306         0        *
</TABLE>


------------------

*    Less than 1%.


(1)  Paradigm Group, L.L.C. is controlled by Sheldon Drobny.

(2)  Consists of warrants to purchase an aggregate of 75,000 shares of our
     common stock.

(3)  Consists of stock units comprised of 29,153 shares of our common stock and
     warrants to purchase an additional 29,153 shares of our common stock.


                              PLAN OF DISTRIBUTION

         The selling shareholders and their pledgees, donees, transferees and
other non-sale transferees may offer their shares at various times in one or
more of the following transactions:

         -     in the Nasdaq National Market;

         -     in the over-the-counter market; or

         -     in privately negotiated transactions

at prevailing market prices at the time of sale, at prices related to those
prevailing market prices, at negotiated prices or at fixed prices.


                                       15
<PAGE>

         The selling shareholders may also sell the shares under Rule 144
instead of under this prospectus, if Rule 144 is available for those sales.


         We will not receive any proceeds from the sale of our common stock by
the selling shareholders.


         The transactions in the shares covered by this prospectus may be
carried out by one or more of the following methods:

         -     ordinary brokerage transactions and transactions in which the
               broker solicits purchasers;

         -     purchases by a broker or dealer as principal, and the resale by
               that broker or dealer for its account as part of the distribution
               under this prospectus, including resale to another broker or
               dealer;

         -     block trades in which the broker or dealer will attempt to sell
               the shares as agent but may position and resell a portion of the
               block as principal in order to facilitate the transaction; or

         -     negotiated transactions between selling shareholders and
               purchasers, with or without a broker or dealer.



         As of the date of this prospectus, we are not aware of any agreement,
arrangement or understanding between any broker or dealer and any of the selling
shareholders with respect to the offer or sale of the shares under this
prospectus.

         We have advised the selling shareholders that, during the time each is
engaged in distributing shares covered by this prospectus, each must comply with
the requirements of the Securities Act and the Exchange Act, including Rule
10b-5 and Regulation M. Under those rules and regulations, they:

         -     may not engage in any stabilization activity in connection with
               our securities;

         -     must furnish each broker that offers common stock covered by this
               prospectus with the number of copies of this prospectus that are
               required by each broker; and

         -     may not bid for or purchase any of our securities or attempt to
               induce any person to purchase any of our securities other than as
               permitted under the Exchange Act.

         Under the terms of each of the warrants, we have agreed to indemnify
and hold harmless each selling shareholder against liabilities under the
Securities Act, which may be based upon, among other


                                       16
<PAGE>

things, any untrue statement or alleged untrue statement of a material fact or
any omission or alleged omission of a material fact, unless made or omitted in
reliance upon written information provided to us by that selling shareholder for
use in this prospectus. We have agreed to bear the expenses incident to the
registration of the shares, other than selling discounts and commissions.

                 INDEMNIFICATION FOR SECURITIES ACT LIABILITIES

         Our Amended and Restated Articles of Organization eliminate, subject to
certain exceptions, the personal liability of our directors for monetary damages
for breaches of fiduciary duties as directors. Our Restated Articles do not
provide for the elimination of, or any limitation on, the personal liability of
a director for (i) any breach of the director's duty of loyalty to Boston
Biomedica and our shareholders; (ii) acts or omissions not in good faith or
which involve intentional misconduct or a knowing violation of law; (iii)
certain unauthorized dividends, redemptions or distributions as provided under
Section 61 of the Massachusetts Business Corporation Law; (iv) certain loans of
company assets to any of our officers or directors as provided under Section 62
of the Massachusetts Business Corporation Law; or (v) any transaction from which
the director derived an improper personal benefit. This provision of our Amended
and Restated Articles of Organization will limit the remedies available to you
in the event of breaches of any director's duties to Boston Biomedica and our
shareholders. Our Amended and Restated Articles of Organization provide that we
may, either in our by-laws or by contract, provide for the indemnification of
directors, officers, employees and agents, by whomever elected or appointed, to
the full extent permitted by law.

         Insofar as indemnification for liabilities arising under the Securities
Act of 1933 may be permitted to our directors, officers or controlling persons
pursuant to the foregoing provisions, or otherwise, we have been informed that
in the opinion of the Securities and Exchange Commission such indemnification is
against public policy as expressed in the Securities Act and is, therefore,
unenforceable.

                                  LEGAL MATTERS

         For the purpose of this offering, Brown, Rudnick, Freed & Gesmer,
Boston, Massachusetts, will pass upon the validity of the shares of common stock
covered under this prospectus.


                                       17
<PAGE>

                                     EXPERTS

         The financial statements incorporated in this prospectus by reference
to the Annual Report on Form 10-K for the year ended December 31, 1999 have been
so incorporated in reliance on the report of PricewaterhouseCoopers LLP,
independent accountants, given on the authority of said firm as experts in
auditing and accounting.

                       WHERE YOU CAN FIND MORE INFORMATION

         We file annual, quarterly and special reports, proxy statements and
other information with the SEC. You may read and copy any document we file at
the SEC's public reference rooms at 450 Fifth Street, N.W., Washington, D.C.,
20549, in Chicago, Illinois and in New York, New York. Please call the SEC at
1-800-SEC-0330 for further information on the public reference rooms. Our SEC
filings are also available to the public over the Internet on the SEC's website
at http://www.sec.gov.


         We have filed with the SEC a registration statement on Form S-3 under
the Securities Act of 1933, as amended, with respect to the common stock offered
in connection with this prospectus. This prospectus does not contain all of the
information set forth in the registration statement. We have omitted parts of
the registration statement in accordance with the rules and regulations of the
SEC. For further information with respect to us and our common stock, you should
refer to the registration statement and to the exhibits and schedules filed as
part of the registration statement, as well as the documents discussed below.
Statements contained in this prospectus as to the contents of any contract or
other document are not necessarily complete and, in each instance, you should
refer to the copy of the contract or document filed as an exhibit to or
incorporated by reference in the registration statement. Each statement as to
the contents of any contract or document is qualified in all respects by
reference to the contract or document itself. You may obtain copies of the
registration statement from the SEC's principal office in Washington, D.C. upon
payment of the fees prescribed by the SEC, or you may examine the registration
statement without charge at the offices of the SEC described above.


         The SEC allows us to "incorporate by reference" the information that we
file with it, which means that we can disclose important information to you by
referring you to those documents. The information incorporated by reference is
considered to be part of this prospectus, and information that we file later


                                       18
<PAGE>

with the SEC will automatically update and supersede this information. We
incorporate by reference the following documents:

         -     Our Annual Report on Form 10-K for the fiscal year ended December
               31, 1999;

         -     Our Quarterly Report on Form 10-Q for the fiscal quarter ended
               March 31, 2000;


         -     Our Quarterly Report on Form 10-Q for the fiscal quarter ended
               June 30, 2000; and


         -     The description of our common stock contained in our registration
               statement on Form 8-A dated October 25, 1996.

We also incorporate by reference any future filings made with the SEC under
Sections 13(a), 13(c), 14 or 15(d) of the Securities Exchange Act of 1934, as
amended, prior to the termination of the offering to which this prospectus
relates.

         You may request a copy of any or all of these filings, at no cost, by
writing or telephoning us at the following address:

                           Boston Biomedica, Inc.
                           375 West Street
                           West Bridgewater, MA  02379
                           (508) 580-1900
                           Attn: Investor Relations


                                       19
<PAGE>

THIS PROSPECTUS IS PART OF A REGISTRATION STATEMENT WE FILED WITH THE SEC. YOU
SHOULD RELY ONLY ON THE INFORMATION OR REPRESENTATIONS PROVIDED IN THIS
PROSPECTUS. WE HAVE NOT AUTHORIZED ANYONE TO PROVIDE YOU WITH ANY INFORMATION
THAT IS NOT CONTAINED IN THIS PROSPECTUS. THE SELLING SHAREHOLDERS DESCRIBED IN
THIS PROSPECTUS ARE NOT MAKING AN OFFER TO SELL OR SOLICITING AN OFFER TO BUY
ANY SHARES IN ANY JURISDICTION WHERE THE OFFER OR SALE IS NOT PERMITTED. YOU
SHOULD NOT ASSUME THAT THE INFORMATION IN THIS PROSPECTUS IS ACCURATE AS OF ANY
DATE OTHER THAN THE DATE OF THIS PROSPECTUS.


                       -----------------
                       TABLE OF CONTENTS
                       -----------------


Summary                                                   3
Risk Factors                                              4
Warnings Regarding Forward-Looking Statements            14
Use of Proceeds                                          14
Selling Shareholders                                     16
Plan of Distribution                                     17
Indemnification for Securities Act Liabilities           19
Legal Matters                                            19
Experts                                                  20
Where You Can Find More Information                      20


        BOSTON BIOMEDICA, INC.




 Up to 633,306 Shares of Common Stock




              PROSPECTUS
        (Subject to Completion)


                                      II-1
<PAGE>

                                     PART II
                     INFORMATION NOT REQUIRED IN PROSPECTUS

ITEM 14.   OTHER EXPENSES OF ISSUANCE AND DISTRIBUTION

The following table sets forth the various expenses payable by us in connection
with the sale and distribution of the securities registered hereby. All amounts
are estimated except the SEC and Nasdaq fees. We will bear all of the costs of
issuance and distribution as follows:


<TABLE>
          <S>                                                                          <C>
          SEC Registration Fee...................................................      $     481
          Nasdaq Filing Fee......................................................      $  17,500
          Accounting Fees and Expenses...........................................      $  35,000
          Legal Fees and Expenses................................................      $  50,000
          Costs of Printing and Engraving                                              $   1,000
          Miscellaneous..........................................................      $     519
                                                                                       =========
                   Total.........................................................      $104,5000
</TABLE>


ITEM 15.  INDEMNIFICATION OF DIRECTORS AND OFFICERS

Our amended and restated by-laws include provisions to permit the
indemnification of our officers and directors for damages arising out of the
performance of their duties unless such damages arise out of the officer's or
director's failure to exercise his duties and to discharge the duties of his
office in good faith and in the reasonable belief that his action was in, or not
opposed to, the best interest of Boston Biomedica, and with respect to any
criminal action or proceeding, do not have reasonable cause to believe that his
conduct was unlawful.

ITEM 16.    EXHIBITS


<TABLE>
<CAPTION>
EXHIBIT
NUMBER
-------

<S>             <C>                                                                             <C>
4.1             Description of certificate for shares of Boston Biomedica common stock                 *
4.2             Form of Warrant Certificate                                                            **
5.1             Legal Opinion of Brown, Rudnick, Freed & Gesmer, P.C.                           previously filed
23.1            Consent of PricewaterhouseCoopers LLP                                            filed herewith
23.2            Consent of Brown, Rudnick, Freed & Gesmer, P.C. (included in Exhibit 5.1)       previously filed
24.1            Power of Attorney                                                               previously filed
</TABLE>

----------

*The above exhibit was previously filed as an exhibit of the same number to our
registration statement on Form S-1 (registration no. 333-10759), as amended,
filed on August 23, 1996 and is incorporated herein by reference.

**The above exhibit was previously filed as exhibit number 4.3 to our quarterly
report on Form 10-Q for the period ended September 30, 1999, and is incorporated
herein by reference.


                                      II-2
<PAGE>

ITEM 17.  UNDERTAKINGS

    (a)  The undersigned registrant hereby undertakes:

        (1) To file, during any period in which offers or sales are being made,
    a post-effective amendment to this registration statement to include any
    material information with respect to the plan of distribution not previously
    disclosed in the registration statement or any material change to such
    information in the registration statement;

        (2) That, for the purpose of determining any liability under the
    Securities Act of 1933, each such post-effective amendment shall be deemed
    to be a new registration statement relating to the securities offered
    therein, and the offering of such securities at that time shall be deemed to
    be the initial BONA FIDE offering thereof; and

        (3) To remove from registration by means of a post-effective amendment
    any of the securities being registered which remain unsold at the
    termination of the offering.

    (b) The undersigned registrant hereby undertakes that, for purposes of
determining any liability under the Securities Act of 1933, each filing of the
registrant's annual report pursuant to Section 13(a) or Section 15(d) of the
Securities Exchange Act of 1934 (and, where applicable, each filing of an
employee benefit plan's annual report pursuant to Section 15(d) of the
Securities Exchange Act of 1934) that is incorporated by reference in the
registration statement shall be deemed to be a new registration statement
relating to the securities offered therein, and the offering of such securities
at that time shall be deemed to be the initial BONA FIDE offering thereof.

    (c) Not applicable.

    (d) Not applicable.

    (e) Not applicable.

    (f) Not applicable.

    (g) Not applicable.

    (h) Insofar as indemnification for liabilities arising under the Securities
Act of 1933 may be permitted to directors, officers and controlling persons of
the registrant pursuant to the foregoing provisions, or otherwise, the
registrant has been advised that in the opinion of the SEC such indemnification
is against public policy as expressed in the Securities Act of 1933 and is,
therefore, unenforceable. In the event that a claim for indemnification against
such liabilities (other than the payment by the registrant of expenses incurred
or paid by a director, officer or controlling person of the registrant in the
successful defense of any action, suit or proceeding) is asserted by such
director, officer or controlling person in connection with the securities being
registered, the registrant will, unless in the opinion of its counsel the matter
has been settled by controlling precedent, submit to a court of appropriate
jurisdiction the question of whether such indemnification by it is against
public policy as expressed in the Securities Act of 1933 and will be governed by
the final adjudication of such issue.

    (i) Not applicable.

    (j) Not applicable.


                                      II-3
<PAGE>

                                   SIGNATURES


Pursuant to the requirements of the Securities Act of 1933, the registrant
certifies that it has reasonable grounds to believe that it meets all the
requirements for filing on Form S-3 and has duly caused this pre-effective
amendment number 2 to the registration statement to be signed on its behalf by
the undersigned, thereunto duly authorized, in the Town of West Bridgewater,
Commonwealth of Massachusetts, on September 1, 2000.


                                              BOSTON BIOMEDICA, INC.

                                              By: /s/ Richard T. Schumacher
                                                  ------------------------------
                                                  Richard T. Schumacher,
                                                  Chief Executive Officer


    PURSUANT TO THE REQUIREMENTS OF THE SECURITIES ACT OF 1933, THIS
PRE-EFFECTIVE AMENDMENT NUMBER 2 TO THE REGISTRATION STATEMENT HAS BEEN SIGNED
BY THE FOLLOWING PERSONS IN THE CAPACITIES AND ON THE DATES INDICATED.

<TABLE>
<CAPTION>
                    SIGNATURE                                       TITLE                                 DATE

<S>                                                 <C>                                             <C>
         /s/ Richard T. Schumacher                  Director and Principal Executive                September 1, 2000
--------------------------------------------            Officer
         Richard T. Schumacher


                  *                                 Director and Principal Financial and            September 1, 2000
--------------------------------------------            Accounting Officer
         Kevin W. Quinlan


                  *
--------------------------------------------        Director                                        September 1, 2000
         Francis E. Capitanio


                  *
--------------------------------------------        Director                                        September 1, 2000
         Calvin A. Saravis, Ph.D.

                  *
--------------------------------------------        Director and Treasurer                          September 1, 2000
William R. Prather, R.Ph., M.D.
</TABLE>


*        By: /s/ Richard T. Schumacher
             -----------------------------------
             Richard T. Schumacher,
             Attorney-in-Fact


<PAGE>

                                  EXHIBIT INDEX


<TABLE>
<CAPTION>
EXHIBIT
NUMBER
-------
<S>             <C>                                                                             <C>
4.1             Description of certificate for shares of Boston Biomedica common stock                  *
4.2             Form of Warrant Certificate                                                            **
5.1             Legal Opinion of Brown, Rudnick, Freed & Gesmer, P.C.                           previously filed
23.1            Consent of PricewaterhouseCoopers LLP                                            filed herewith
23.2            Consent of Brown, Rudnick, Freed & Gesmer, P.C. (included in Exhibit 5.1)       previously filed
24.1            Power of Attorney                                                               previously filed
</TABLE>



----------

*The above exhibit was previously filed as an exhibit of the same number to our
registration statement on Form S-1 (registration no. 333-10759), as amended,
filed on August 23, 1996 and is incorporated herein by reference.

**The above exhibit was previously filed as exhibit number 4.3 to our quarterly
report on Form 10-Q for the period ended September 30, 1999, and is incorporated
herein by reference.


                                      E-1