<PAGE>   1
                             WASHINGTON, D.C. 20549
                                    FORM 10-Q

[X]     QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES
        EXCHANGE ACT OF 1934

                  For the quarterly period ended June 30, 2000.

                                       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: 0-29975

                            ACLARA BIOSCIENCES, INC.
             (Exact name of registrant as specified in its charter)

        DELAWARE                                         94-3222727
(State of Incorporation)                    (I.R.S. Employer Identification No.)

                                1288 PEAR AVENUE
                         MOUNTAIN VIEW, CALIFORNIA 94034
              (Address of principal executive offices and zip code)

                                 (650) 210-1200
              (Registrant's telephone number, including area code)



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

The number of shares outstanding of the registrant's common stock as of July 31,
2000 was 34,488,276.

<PAGE>   2

                            ACLARA BIOSCIENCES, INC.

                                TABLE OF CONTENTS

<TABLE>
<CAPTION>

<S>               <C>
PART 1:           FINANCIAL INFORMATION

        Item 1.   Financial Statements (unaudited):

                  Condensed Balance Sheets as of June 30, 2000 and
                  December 31, 1999.                                            3

                  Condensed Statements of Operations for the three months and
                  six months ended June 30, 2000 and June 30, 1999              4

                  Condensed Statements of Cash Flows for the six months
                  ended June 30, 2000 and June 30, 1999                         5

                  Notes to Condensed Financial Statements                       6

        Item 2.   Management's Discussion and Analysis of Financial
                  Condition and Results of Operations                           9

        Item 3.   Quantitative and Qualitative Disclosures About
                  Market Risk                                                   20



PART II:          OTHER INFORMATION

        Item 1.   Legal Proceedings                                             21

        Item 2.   Changes in Securities and Use of Proceeds.                    22

        Item 3.   Defaults Upon Senior Securities (not applicable)

        Item 4.   Submission of Matters to a Vote of Security Holders
                  (not applicable)

        Item 5.   Other Information (not applicable)

        Item 6.   Exhibits and Reports on Form 8-K.                             23

SIGNATURES                                                                      24

EXHIBIT INDEX                                                                   25
</TABLE>


                                                                          Page 2
<PAGE>   3
                            ACLARA BIOSCIENCES, INC.
                            CONDENSED BALANCE SHEETS
                                 (in thousands)
<TABLE>
<CAPTION>


                                                         June 30,      December 31,
                                                          2000            1999
                                                        ---------      ------------
                                                       (unaudited)

                     ASSETS

Current assets:
<S>                                                     <C>             <C>
    Cash and cash equivalents                           $ 159,893       $  10,250
    Short-term investments                                 48,506           3,479
    Accounts receivable                                       596             615
    Prepaid expenses and
      other current assets                                  1,195             434
                                                        ---------       ---------

Total current assets                                      210,190          14,778

Property and equipment, net                                 5,431           5,171

Restricted cash                                               625             625
Other assets, net                                              43              --
                                                        ---------       ---------

Total assets                                            $ 216,289       $  20,574
                                                        =========       =========

LIABILITIES, MANDATORILY REDEEMABLE CONVERTIBLE
 STOCK & STOCKHOLDERS' EQUITY (DEFICIT)

Current liabilities:
    Accounts payable                                    $     605       $     412
    Accrued payroll and related expenses                      633             114
    Accrued expenses                                        2,505           1,090
    Current portion of capital lease obligations              258             286
    Current portion of loans payable                        1,009             820
                                                        ---------       ---------


Total current liabilities                                   5,010           2,722

Capital lease obligations, less current portion               193             284
Loans payable, less current portion                         2,535           3,087
                                                        ---------       ---------


Total liabilities                                           7,738           6,093
                                                        ---------       ---------
Mandatorily redeemable convertible preferred stock              0          40,973
                                                        ---------       ---------

Stockholders' Equity (Deficit)
    Common stock                                               35               2
    Additional paid-in capital                            253,810           2,589
    Deferred stock-based compensation                     (14,980)         (6,508)
    Notes receivable for common stock                        (641)             (7)
    Accumulated other comprehensive income                    775               4
    Deficit accumulated during development stage          (30,448)        (22,572)
                                                        ---------       ---------
Total stockholders' equity (deficit)                      208,551         (26,492)
                                                        ---------       ---------

Total liabilities, mandatorily redeemable
 convertible stock and stockholders'
 equity (deficit)                                       $ 216,289       $  20,574
                                                        =========       =========
</TABLE>

The accompanying notes are an integral part of these financial statements.


                                                                          Page 3
<PAGE>   4


                            ACLARA BIOSCIENCES, INC.
                        CONDENSED STATEMENT OF OPERATIONS
                      (in thousands, except per share data)
                                   (Unaudited)

<TABLE>
<CAPTION>

                                                    Three Months Ended            Six Months Ended
                                                         June 30,                      June 30,
                                                    2000           1999           2000           1999
                                                  --------       --------       --------       --------
<S>                                               <C>            <C>            <C>            <C>
REVENUE:
Grant and collaboration                            $   950        $   774       $  1,790        $ 1,145
                                                   -------        -------       --------        -------
     Total revenue                                     950            774          1,790          1,145
                                                   -------        -------       --------        -------
OPERATING EXPENSES:
Research and development                             5,611          1,258          9,728          2,859
General and administrative                           3,662            933          6,174          1,579
                                                   -------        -------       --------        -------
      Total operating expenses                       9,273          2,191         15,902          4,438
                                                   -------        -------       --------        -------
Loss from operations                                (8,323)        (1,417)       (14,112)        (3,293)

Interest income                                      3,630            129          3,723            289

Interest expense                                      (173)           (23)          (461)          (206)
                                                   -------        -------       --------        -------

Net loss                                           $(4,866)       $(1,311)      $(10,850)       $(3,210)
                                                   =======        =======       ========        =======
Net loss per common share
 -- basic and diluted                              $ (0.15)       $ (0.87)      $  (0.32)       $ (2.13)

Shares used in net loss per common
share calculations - basic and diluted              33,459          1,514         33,445          1,504
</TABLE>

The accompanying notes are an integral part of these financial statements.


                                                                          Page 4
<PAGE>   5

                            ACLARA BIOSCIENCES, INC.
                        CONDENSED STATEMENT OF CASH FLOWS
                                 (in thousands)
                                   (Unaudited)
<TABLE>
<CAPTION>

                                                                              Six Months Ended
                                                                                  June 30,
                                                                            2000            1999
                                                                          ---------       ---------
<S>                                                                       <C>             <C>
CASH FLOWS FROM OPERATING ACTIVITIES:
Net loss                                                                   $(10,850)        $(3,210)
Adjustments to reconcile net loss to net cash used in
operating activities:
Depreciation and amortization                                                   428             206
Amortization of long-term debt discount                                          56               0
Amortization of deferred compensation                                         3,655             306
Changes in assets and liabilities:
   Accounts receivable                                                           19             140
   Prepaid expenses and other current assets                                   (761)           (165)
   Accounts payable                                                             192           1,389
   Accrued payroll and related expenses                                         519             202
   Accrued expenses and other liabilities                                     1,250           1,102
   Deferred revenue                                                              94              70
                                                                           --------         -------
      Net cash used in operating activities                                  (5,398)             40
                                                                           --------         -------
CASH FLOWS FROM INVESTING ACTIVITIES:
Acquisition of property and equipment                                          (688)         (3,159)
Purchase of short-term investments                                          (44,255)         (6,582)
Change in other assets                                                          (44)             30
                                                                           --------         -------
      Net cash used in investing activities                                 (44,987)         (9,711)
                                                                           --------         -------
CASH FLOWS FROM FINANCING ACTIVITIES:
Principal payments under capital lease obligations                             (119)              0
Repayment of loans payable                                                     (346)         (2,419)
Proceeds from issuance of loans payable                                           0              20
Proceeds from issuance of preferred stock, net of issuance costs                  0          19,398
Repurchase of Series A preferred stock and one share of common stock              0          (2,713)
Proceeds from initial public offering, net of issuance costs                200,488               0
Proceeds from issuance of common stock                                            5               0
                                                                           --------         -------
      Net cash provided by financing activities                             200,028          14,286
                                                                           --------         -------
Net increase (decrease) in cash and cash equivalents                        149,643           4,615
Cash and cash equivalents, beginning of period                               10,250           1,746
                                                                           --------         -------
Cash and cash equivalents, end of period                                   $159,893         $ 6,361
                                                                           ========         =======
</TABLE>

The accompanying notes are an integral part of these financial statements.

                                                                          Page 5
<PAGE>   6



                            ACLARA BIOSCIENCES, INC.
              NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS
                                   (Unaudited)

1.  BASIS OF PRESENTATION:

    In the opinion of management, the accompanying unaudited condensed financial
statements contain all adjustments (all of which are normal and recurring in
nature) necessary to present fairly the financial position, results of
operations and cash flows of ACLARA BioSciences, Inc. ("ACLARA") for the periods
indicated. Interim results of operations are not necessarily indicative of the
results to be expected for the full year or any other interim periods. The notes
to the financial statements contained in our Registration Statement on Form S-1
for the year ended December 31, 1999 should be read in conjunction with these
condensed financial statements. The balance sheet at December 31, 1999 was
derived from audited financial statements. The preparation of financial
statements in conformity with generally accepted accounting principles requires
management to make estimates and assumptions that affect the reported amounts of
assets and liabilities and disclosure of contingent assets and liabilities at
the date of the financial statements and the reported amounts of expenses during
the reporting period. Actual results could differ from those estimates.

2.  SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES:

    RECENT ACCOUNTING PRONOUNCEMENTS

    In June 1998, the Financial Accounting Standards Board ("FASB") issued
Statement of Financial Accounting Standards No. 133, Accounting for Derivative
instruments and Hedging Activities ("SFAS"). SFAS No. 133 establishes accounting
and reporting standards for derivative instruments, including certain derivative
instruments, embedded in other contracts, and for hedging activities. It
requires that an entity recognize all derivatives as either assets or
liabilities in the statement of financial position and measure those instruments
at fair value. In July 1999, the FASB issued Statement of Financial Accounting
Standards No. 137 Accounting for Derivative Instruments and Hedging Activities-
Deferral of the Effective Date of FASB Statement No. 133 ("SFAS 137"). SFAS 137
deferred the effective date of SFAS 133 until the first fiscal year beginning
after June 15, 2000. We will adopt the standard during January 2001. To date, we
do not engage in hedging activities.

    In December 1999, the Securities and Exchange Commission issued Staff
Accounting Bulletin No. 101, "Revenue Recognition in Financial Statements," or
SAB 101, which provides guidance on the recognition, presentation, and
disclosure of revenue in financial statements filed with the SEC. SAB 101
outlines the basic criteria that must be met to recognize revenue and provides
guidance for disclosures related to revenue recognition policies. ACLARA'S
revenue recognition policy is in compliance with the provisions of SAB 101.

    In March 2000, the Financial Accounting Standards Board issued
Interpretation No. 44 Accounting for Certain Transactions Involving Stock
Compensation -- an interpretation of APB Opinion No. 25 ("FIN 44"). This
interpretation clarifies the definition of employee for purposes of applying
Accounting Practice Board Opinion No. 25, Accounting for Stock Issued to
Employees ("APB 25"), the criteria for determining whether a plan qualifies as a
noncompensatory plan, the accounting consequence of various modifications to the
terms of a previously fixed stock option or award, and the accounting for an
exchange of stock compensation awards in a business combination. This
Interpretation is effective July 1, 2000, but certain conclusions in this
Interpretation cover specific events that occur after either December 15, 1998,
or January 12, 2000. Management believes that FIN 44 will not have a material
effect on the financial position or results of operation of ACLARA.

NET LOSS PER SHARE

    Basic net loss per share is calculated based on the weighted-average number
of common shares outstanding during the period. Diluted net loss per share would
give effect to the dilutive effect of common stock equivalents consisting of
stock options and warrants (calculated using the treasury stock method).
Potentially dilutive securities have been excluded from the diluted net loss per
share computations as they have an antidilutive effect due to our net loss.

    A reconciliation of shares used in the calculations is as follows (in
thousands, except per share data):
                                                                          Page 6

<PAGE>   7


<TABLE>
<CAPTION>

                                                                           Three Months Ended             Six Months Ended
                                                                                 June 30,                       June 30,
                                                                            2000           1999           2000           1999
                                                                          --------       --------       --------       --------
<S>                                                                       <C>            <C>            <C>            <C>
Basic and diluted:
Net loss                                                                   $(4,866)       $(1,311)      $(10,850)       $(3,210)

Weighted average common shares outstanding                                  34,270          1,603         34,081          1,602
Less: weighted average shares subject to repurchase                           (811)           (89)          (636)           (98)
                                                                           -------        -------       --------        -------
Weighted average shares used in basic and diluted net loss per
 share calculations                                                          33,459          1,514         33,445          1,504
                                                                           =======        =======       ========        =======
Net loss per common share  - basic and diluted                             $ (0.15)       $ (0.87)      $  (0.32)       $ (2.13)
</TABLE>


    The following outstanding options and warrants, and convertible preferred
stock (on an as-converted basis), were excluded from the computation of diluted
net loss per share as they had an anti-dilutive effect:

<TABLE>
<CAPTION>

                                  Three Months Ended               Six Months Ended
                                         June 30,                       June 30,
                                   2000            1999           2000            1999
                                 ---------       ---------      ---------       ---------
<S>                              <C>             <C>            <C>             <C>
Options and warrants             3,003,947       3,193,149      2,816,303       2,632,366
Convertible preferred stock              -      18,941,956              -      18,701,635
</TABLE>


INVESTMENTS IN MARKETABLE SECURITIES

    We account for investments in marketable securities in accordance with SFAS
No. 115, "Accounting for Certain Investments in Debt and Equity Securities".
Debt and equity securities are classified as available-for-sale securities and
are reported at fair market value with any unrealized holding gains and losses
excluded from current earnings and reported in stockholders' equity.

3.  LEGAL MATTERS:

    On March 22, 1999, Caliper Technologies Corporation ("Caliper") filed suit
in Superior Court of California, naming as defendants Bertram Rowland
("Rowland"), Flehr, Hohbeck Test, Albritton & Herbert ("Flehr") and ACLARA. The
suit alleges that Rowland and Flehr, who had been and were counsel to us, while
being, for a limited period during this time, also counsel to Caliper, learned
trade secrets of Caliper which were then improperly used by Rowland and Flehr as
counsel to us, and by us, in a patent application that resulted in an issued
patent, and for other unspecified purposes. The suit seeks actual and exemplary
damages and equitable relief. Trial is set to begin on September 11, 2000.

    On April 26, 1999, we filed a patent infringement action against Caliper in
the U.S. District Court in Northern California alleging infringement of our US
Patent No. 5,750,015 (the "015 patent") which concerns methods and devices for
moving molecules by the application of electrical fields. On July 19, 2000 we
announced that the U.S. District Court for the Northern District of California
issued a Markman order interpreting the claims of the `015 patent. Among its
rulings, the Court refused to limit the claims to devices that employed
electrophoretic, but not electroosmotic, movement as Caliper had asserted. The
Court held that, in the context of ACLARA's patent, the term "plurality of
electrodes" defines electrodes that are positioned along the axis of trenches in
microfluidic devices, but not necessarily within the trenches themselves. The
Court also determined that the word "trench" as it appears in the claims of the
`015 is defined as an open structure which does not include a structure that has
been permanently covered. In addition, the Court held that eight of forty-seven
claims in the `015 were indefinite and, therefore, invalid.




                                                                          Page 7
<PAGE>   8



    In January 2000, Caliper filed a complaint against us in the U. S. District
Court of Northern California, alleging infringement of four patents that they
claim to have licensed exclusively. On March 10, 2000, Caliper amended its
lawsuit to include a fifth recently issued patent.

    We have received correspondence from an attorney representing certain
minority shareholders of 2C Optics (our former parent company), alleging
violations of corporate and securities laws by ACLARA and one or more of its
directors, with regards to a repurchase of our Series A preferred stock from 2C
Optics in March, 1999. The attorney is threatening litigation to force us to
sell to his clients shares of ACLARA stock, at $0.60 per share (the price at
which they were re-purchased), equal to each clients' pro rated portion of the
shares repurchased. An attorney representing 2C Optics has informed us that they
are also considering litigation against us based on the same allegations.

    We are currently unable to predict at this time the final outcome of these
matters and the ultimate effect, if any, on ACLARA's financial condition, cash
flows and results of operations.


                                                                          Page 8
<PAGE>   9


ITEM 2. MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS
        OF OPERATIONS

    Statements in this Management's Discussion and Analysis of Financial
Condition and Results of Operations which express that ACLARA ("ACLARA", "we,"
"us" or "our") "believes," "anticipates," "expects," "intends," or "plans to",
as well as other statements which are not historical fact, are forward-looking
statements within the meaning of the Private Securities Litigation Reform Act of
1995. Actual events or results may differ materially as a result of the risks
and uncertainties described herein and elsewhere including, in particular, those
factors described under "Additional Factors That Might Affect Future Results"
set forth below.

    The following discussion of the financial condition and results of
operations should be read in conjunction with our financial statements and the
accompanying notes to those statements.

OVERVIEW

    We are a developer of microfluidic lab-on-a-chip technology, having access
to a wide range of technology and intellectual property required to broadly
address the genomics and pharmaceutical drug screening markets. We are
developing advanced tools for drug discovery and genomics using our proprietary
microfluidic array technology and assay chemistries. By performing integrated
sample processing and analysis on plastic microfluidic array LabCard chips,
these tools would enable the rapid, parallel processing of large numbers of
samples while requiring only minute volumes of expensive or rare reagents.

    We were formed by a spin-off transaction from Soane Technologies, Inc. and
incorporated in Delaware in 1995 under the name Soane BioSciences, Inc. In 1998,
we changed our name to ACLARA BioSciences, Inc. Since our inception, we have
engaged primarily in organization and research and development efforts related
to the application of microfluidics technology to genomics and pharmaceutical
drug screening. To date, we have generated most of our revenues from research
partnerships and collaborations and from government grants. Our partners and
collaborators include PE Biosystems, Packard BioScience, the R.W. Johnson
Pharmaceutical Research Institute, a subsidiary of Johnson & Johnson, and
Cellomics, Inc. We have also received government grants from the National
Institutes of Health (NIH), the National Institute of Standards and Technology
Advanced Technology Program (NIST ATP) and the Defense Advance Research Projects
Agency (DARPA).

    On March 24, 2000 ACLARA completed its initial public offering, selling
10,350,000 shares of common stock.

    We have invested substantial amounts in establishing our microfluidics
technologies. Since our inception we have spent over $20 million on our research
and development efforts. Over 85% of our 90 employees at June 30, 2000 were
engaged in research and development.

    We have incurred significant losses since our inception. As of June 30,
2000, our accumulated deficit was $30.4 million and total stockholders' equity
was $208.6 million. We expect to incur additional operating losses over at least
the next two years as we continue to expand our research and development efforts
and infrastructure.

    Our sources of potential revenue for the next several years are likely to be
payments under existing and possible future collaborative arrangements,
government research grants, product revenue from the sale of LabCard products,
and royalties from our collaborators based on revenue received from the sale of
equipment and reagents utilizing our technology.

    We recognize grant and collaboration revenue based on meeting certain
requirements, completing milestones as specified in the grants or contracts,
straight line over the period of certain contracts or as work is performed and
evidenced by time sheets and expense reports for certain grants. Revenue on
product sales will be recognized upon shipment of product to the customer.
Revenue on license agreements will be recognized on a straight line basis over
the life of services to be rendered under the license agreements.


                                                                          Page 9
<PAGE>   10



    We account for equity instruments issued to non-employees in accordance with
the provisions of SFAS 123 and Emerging Issues Task Force Issue No. 96-18,
"Accounting for Equity Instruments That Are Issued to Other Than Employees for
Acquiring, or in Conjunction with Selling, Goods or Services."

    We account for stock-based employee compensation arrangements in accordance
with provisions of Accounting Principles Board Opinion No. 25, "Accounting for
Stock Issued to Employees" ("APB No. 25") and comply with the disclosure
provisions of Statement of Financial Accounting Standards No. 123, "Accounting
for Stock-Based Compensation" ("SFAS No. 123").

    Under APB No. 25, compensation expense is based on the difference, if any on
the date of the grant, between the fair value of our stock and the exercise
price. SFAS No. 123 defines a "fair value" based method of accounting for an
employee stock option or similar equity instrument. We recorded amortization of
deferred compensation of approximately $2.0 million for the three months ended
June 30, 2000 and approximately $3.7 million for the six months ended June 30,
2000 to the appropriate operating expense categories. The amortization expense
relates to options awarded to employees in all operating expense categories.


RESULTS OF OPERATIONS

        Revenue. Our revenue for the three months ended June 30, 2000 was
$950,000, an increase of $176,000 or 23% from $774,000 for the prior year
period. Our revenue for the six months ended June 30, 2000 was $1.8 million, an
increase of $645,000 or 56% from $1.1 million for the prior year period. The
increase resulted entirely from revenue from the collaboration agreement with PE
Biosystems and Johnson & Johnson, our agreement with Cellomics, and our grant
from NIST ATP to develop LabCard systems for nucleic acid sample processing,
offset by decreased revenue from an existing research and development contract
with DARPA which is nearing completion.

        Research and Development. Research and development expenses were $5.6
million for the three months ended June 30, 2000 and $1.3 million for the prior
year period. Of the $4.3 million increase, $1.6 million was related to non-cash
stock-based compensation expense. Research and development expenses were $9.7
million for the six months ended June 30, 2000 and $2.9 million for the prior
year period. Of the $6.9 million increase, $3.0 million was related to non-cash
stock-based compensation expense. The remaining increases were due to increased
staffing in R&D and pilot manufacturing, and other project and personnel related
costs. We expect to continue to devote substantial resources to research and
product development, and we expect that research and development expenses will
continue to increase on an absolute dollar value basis.

        General and Administrative. General and administrative expenses were
$3.7 million for the three months ended June 30, 2000, as compared to $933,000
during the same period of the previous year. Of the $2.7 million increase,
$160,000 was related to non-cash stock-based compensation expense. General and
administrative expenses were $6.2 million for the six months ended June 30, 2000
and $1.6 million for the prior year period. Of the $4.6 million increase,
$318,000 was related to non-cash stock-based compensation expense. The remaining
increase was due to on-going intellectual property matters, administrative costs
associated with R&D growth, and general corporate expenses associated with
becoming a public company. We expect that general and administrative expenses
will increase in absolute dollar amounts as we expand our administrative staff,
move into office space vacated by sublessees and incur additional costs related
to being a public company, including directors' and officers' insurance,
investor relations programs and increased professional fees.

        Interest Income (Expense). Interest income represents income earned on
our cash and cash equivalents and short term investments; interest expense
represents interest paid on loans and capital leases. Interest income was $3.6
million for the three month period ended June 30, 2000, and $129,000 for the
prior year period. Interest income was $3.7 million for the six months ended
June 30, 2000, and $289,000 for the prior year period. The increase was due to
higher average cash balances as a result of our recent stock offering. Interest
expense was $173,000 for the three months ended June 30, 2000, and $23,000 for
the prior year period. Interest expense was $461,000 for the six months period
ended June 30, 2000, and $206,000 for the prior year period. The increase was
due to interest incurred on loans for tenant improvements and related equipment
at our new Mountain View facility.

        Net Loss. Net loss was $4.9 million for the three months ended June 30,
2000 compared to a loss of $1.3 million for the period ended June 30, 1999. Net
loss was $10.9 million for the six months ended



                                                                         Page 10
<PAGE>   11



June 30, 2000 compared to a loss of $3.2 million for the six months ended June
30, 1999. Net loss for the current period reflects an increase in collaboration
and grant revenue, which was more than offset by increased operating expenses in
research and product development activities, amortization of non-cash
stock-based compensation, on-going intellectual property matters, and general
corporate activities.

LIQUIDITY AND CAPITAL RESOURCES

        On June 30, 2000, we had $208.4 million in cash and cash equivalents and
short-term investments. In addition, we had $1.3 million available on a loan
agreement with a financial institution to be used for the purchase of equipment.

        Net cash used in operating activities for the six months ended June 30,
2000 was $5.4 million. Cash used in operating activities for the six months
ended June 30, 1999 was $40,000. The increase in cash used by operating
activities year-over-year was primarily due to the net loss of $10.9 million for
2000 compared to a net loss in 1999 of $3.2 million, partially offset by an
increase in the amortization of deferred compensation amounts
period-over-period.

        Net cash used in investing activities for the six months ended June 30,
2000 was $45.0 million, compared with $9.7 million for the six months ended June
30, 1999. The proceeds from the sale of the 10,350,000 shares of common stock we
offered during our initial public offering in March 2000 were approximately
$200.5 million after deducting the underwriting discounts and commissions and
other offering expenses. These proceeds were used to purchase short-term
investments or were held as cash and cash equivalents. We believe that our
current cash balances, cash equivalents, short-term investments and cash
generated from our collaborative arrangements and product sales will be
sufficient to meet our operating and capital requirements through the end of
2001. Our capital commitments for the next 12 months, including lease payments,
loan payments, planned tenant improvements, and planned equipment purchases are
estimated to be $6.9 million. Our future liquidity and capital requirements will
depend on numerous factors, including our success in commercializing our
products, the ability of our outside manufacturers to meet our demands at
currently estimated prices, obtaining and enforcing patents important to our
business, and possible technology acquisitions.



                                                                         Page 11


<PAGE>   12

RECENT ACCOUNTING PRONOUNCEMENTS

    In June 1998, the Financial Accounting Standards Board ("FASB") issued
Statement of Financial Accounting Standards No. 133, "Accounting for Derivative
Instruments and Hedging Activities" ("SFAS"). SFAS No. 133 establishes
accounting and reporting standards for derivative instruments, including certain
derivative instruments, embedded in other contracts, and for hedging activities.
It requires that an entity recognize all derivatives as either assets or
liabilities in the statement of financial position and measure those instruments
at fair value. In July 1999, the FASB issued Statement of Financial Accounting
Standards No. 137 "Accounting for Derivative Instruments and Hedging Activities
- Deferral of the Effective Date of FASB Statement No. 133" ("SFAS 137"). SFAS
137 deferred the effective date of SFAS 133 until the first fiscal year
beginning after June 15, 2000. We will adopt the standard during January 2001.
To date, we do not engage in hedging activities.

    In December 1999, the Securities and Exchange Commission issued Staff
Accounting Bulletin No. 101, "Revenue Recognition in Financial Statements," or
SAB 101, which provides guidance on the recognition, presentation, and
disclosure of revenue in financial statements filed with the SEC. SAB 101
outlines the basic criteria that must be met to recognize revenue and provides
guidance for disclosures related to revenue recognition policies. ACLARA's
revenue recognition policy is in compliance with the provisions of SAB 101.

    In March 2000, the Financial Accounting Standards Board issued
Interpretation No. 44 Accounting for Certain Transactions Involving Stock
Compensation - an interpretation of APB Opinion No. 25 ("FIN 44"). This
interpretation clarifies the definition of employee for purposes of applying
Accounting Practice Board Opinion No. 25, Accounting for Stock Issued for
Employees ("APB 25"), the criteria for determining whether a plan qualifies as a
noncompensatory plan, the accounting consequence of various modifications to the
terms of a previously fixed stock option or award, and the accounting for an
exchange of stock compensation awards in a business combination. This
interpretation is effective July 1, 2000, but certain conclusions in this
Interpretation cover specific events that occur after either December 15, 1998,
or January 12, 2000. Management believes that FIN 44 will not have a material
effect on the financial position or results of operation of ACLARA.

               ADDITIONAL FACTORS THAT MIGHT AFFECT FUTURE RESULTS

    The following risk factors outline certain risks and uncertainties
concerning future results and should be read in conjunction with the information
contained in this Quarterly Report on Form 10-Q. Any of these risk factors could
materially and adversely affect our business results of operations, financial
condition and future growth prospects. Additional risks and uncertainties that
we do not currently know about or that we currently deem immaterial may also
impair our business, financial condition, results of operations and future
growth prospects.

WE HAVE A HISTORY OF OPERATING LOSSES AND AN ACCUMULATED DEFICIT, AND WE MAY NOT
ACHIEVE OR MAINTAIN PROFITABILITY IN THE FUTURE.

    Since we were founded in May 1995, we have engaged primarily in research and
development efforts. We have incurred operating losses every year, and we may
never achieve profitability. Net loss for the six months ended June 30, 2000 was
$10.9 million. Net losses for the years ended December 31, 1997, 1998 and 1999
were $2.0 million, $5.5 million, and $8.2 million, respectively. As of June 30,
2000, we had an accumulated deficit of $30.4 million. Our losses have resulted
principally from costs incurred in connection with our research and development
activities and from general and administration costs associated with our
operations.

    We have not commercially launched any LabCard products to date and do not
expect to do so until late 2000. Our ability to generate revenues from product
sales or to achieve profitability is dependent on our ability, alone or with our
collaborative partners, to successfully design, develop, manufacture and
commercialize our microfluidic LabCard products and systems in a timely manner.
Our revenue to date has been generated principally from collaborative research
and development agreements, government grants and interest on cash and
investment balances. We expect that our costs will continue to exceed our
revenues on an annual basis for at least the next two years. Even if we do
achieve profitability, we may not be able to sustain or increase profitability
on a quarterly or annual basis.



                                                                         Page 12
<PAGE>   13

OUR OPERATING RESULTS MAY FLUCTUATE SIGNIFICANTLY.

    Our operating results have fluctuated in the past and are likely to do so in
the future. These fluctuations could cause our stock price to decline. Some of
the factors that could cause our operating results to fluctuate include:

    -   expiration or termination of contracts with collaborators or government
        research grants, which may not be renewed or replaced;

    -   outcome of litigation proceedings to which we are currently a party or
        pending or threatened claims against us;

    -   the timing and willingness of collaborators to commercialize our
        products;

    -   the timing, release and competitiveness of our products; and

    -   general and industry-specific economic conditions, which may affect our
        customers' research and development expenditures and use of our
        products.

    If revenue declines in a quarter, whether due to a delay in recognizing
expected revenue or otherwise, our earnings will decline because many of our
expenses are relatively fixed in the short-term. In particular, research and
development and general and administrative expenses are not affected directly by
variations in revenue.

    Due to fluctuations in our revenue and operating expenses, we believe that
period-to-period comparisons to results of historical operations are not a good
indication of our future performance. It is possible that in some future quarter
or quarters, our operating results will be below the expectations of securities
analysts or investors. In that case, our stock price could fluctuate
significantly or decline.


OUR PRODUCTS ARE IN THE DEVELOPMENT STAGE AND MAY NOT SUCCESSFULLY BE BROUGHT TO
COMMERCIALIZATION.

        We currently have no commercially available products and we have never
developed, manufactured, distributed or sold LabCard products or commercial
systems using our microfluidics technology. We are developing products that are
in many cases part of complex systems that also have not been fully developed,
tested, manufactured or commercially introduced by our major collaborative
partner. We may not be able to perfect the design of our products due to the
complexity of the systems they are part of and/or the demands of the scientific
processes that they address. For instance, we have not yet established the high
degrees of accuracy, reliability and ease of use required for commercial
introduction of our products. Even though we have designed products that
function in a prototype system or on a limited volume basis, we cannot assure
you that we will be able to adapt the design to allow for large-scale
manufacturing and commercialization. Although we have projected launch periods
for certain of our products, we cannot assure you that we will complete
development of the systems by those launch dates, or at all. If we are unable to
design commercially viable LabCard products or systems, either independently or
with our collaborative partners, we may be unable to remain in business.


COMMERCIALIZATION OF OUR PRODUCTS DEPENDS ON MARKET ACCEPTANCE OF OUR LABCARD
CHIPS AND RELATED SYSTEMS. IF THEY DO NOT ACHIEVE ACCEPTANCE, OUR ABILITY TO
GENERATE SALES WILL BE LIMITED AND OUR LOSSES WOULD INCREASE.

    Demand for our LabCard products is substantially dependent upon widespread
market acceptance of systems utilizing our LabCard chips as tools for genomics
and pharmaceutical drug screening. Because most of our LabCard chip products
will be part of larger analytical systems marketed by our collaborative
partners, our ability to sell LabCard chips in these cases depends on adoption
by researchers of entirely new analytical equipment. We cannot assure you that
LabCard chips and related instrument systems using our technology will achieve
substantial acceptance in our target markets. Market acceptance will depend on
many factors, including:

                                                                         Page 13
<PAGE>   14


    -   our ability and the ability of our collaborative partners to demonstrate
        to potential customers the benefits and cost-effectiveness of our
        LabCard chips and systems, relative to products available at the time
        these systems are introduced; and

    -   the extent and success of our partners' efforts to market, sell and
        distribute the LabCard chips and systems.

    Further, if our initial LabCard systems are not favorably received by the
market, it could undermine our ability to successfully introduce subsequent
LabCard chips or systems as well. If our LabCard chips and systems do not gain
market acceptance, our losses would increase and we may be unable to remain in
business.


WE PREDOMINANTLY DEPEND ON COLLABORATIVE PARTNERS TO DEVELOP AND MARKET SYSTEMS
THAT UTILIZE OUR LABCARD CHIPS TO END USERS. IF OUR COLLABORATIVE PARTNERS DO
NOT PERFORM AS EXPECTED, WE MAY BE UNABLE TO DEVELOP AND MARKET OUR PRODUCTS.

    Because the majority of our products are components of larger systems, our
success depends on our ability to establish relationships with collaborative
partners to create products to address market needs. For example, our
collaborative relationship with PE Biosystems provides for the joint development
of systems for genomics research and pharmaceutical drug screening. In this
relationship, we provide LabCard chips as one component of systems used by
researchers for genomics analysis and pharmaceutical drug screening
applications. Our ability to expand the applications for our technology will
largely depend on our ability to broaden our relationship with existing partners
and identify and enter into similar relationships with new collaborative
partners to address additional customer needs. If we are unable to broaden our
existing collaborative relationships or enter into relationships with additional
collaborative partners our business may suffer.

    Our ability to sell products will also depend on the ability of our
collaborative partners to develop instrument systems that can utilize our
LabCard chips. If the development efforts of our collaborative partners fail or
are significantly delayed, our losses would increase. We cannot assure you that
our collaborative partners will be able to develop products as planned.

    We also intend to rely upon our current and future collaborative partners to
market, sell, distribute and promote our LabCard chips. We do not presently
intend to develop a large internal marketing and sales organization.
Accordingly, we will be substantially relying on our collaborative partners to
fulfill these tasks. If our collaborative partners do not perform these
functions satisfactorily, our ability to market, sell and distribute our
products could be severely limited.

    We generally do not have control over the resources or degree of effort that
any of our existing collaborative partners may devote to our collaborations. If
our collaborators breach or terminate their agreements with us or otherwise fail
to conduct their collaborative activities successfully and in accordance with
agreed upon schedules, our business would be harmed. In addition, our
collaborative partners could cease operations, eliminate relevant product lines,
or offer, design, manufacture or promote competing lines of products. Any of
those occurrences would increase our losses.


WE RELY HEAVILY ON PE BIOSYSTEMS TO DEVELOP, MANUFACTURE AND COMMERCIALIZE
SYSTEMS TO BE USED IN CONNECTION WITH OUR LABCARD CHIPS AND TO COMMERCIALIZE
MOST OF OUR LABCARD PRODUCTS. PE BIOSYSTEMS' FAILURE TO DO SO SUCCESSFULLY COULD
DELAY OR PREVENT THE COMMERCIALIZATION OF OUR PRODUCTS IN THE GENOMICS AND
PHARMACEUTICAL DRUG SCREENING MARKETS, AND RESULT IN INCREASED LOSSES.

    As part of our business strategy, we are focusing on the development of our
LabCard chips and related chemistries for genomics and pharmaceutical drug
screening systems. In most cases we are relying on PE Biosystems to manufacture
and commercialize the systems, including commercializing our LabCard chips. We
have collaboration agreements with PE Biosystems to jointly develop microfluidic
systems for genomics and pharmaceutical drug screening. In addition to
developing or co-developing the instrumentation, software and reagents, PE
Biosystems will have the exclusive right to market and sell those products
worldwide. We cannot assure you that PE Biosystems will perform its obligations
under the


                                                                         Page 14
<PAGE>   15

agreements, or that PE Biosystems will successfully commercialize any products
resulting from our joint efforts. Moreover, PE Biosystems has the discretion,
under certain circumstances, to elect not to proceed with the commercialization
of products jointly developed under the agreement. PE Biosystems' failure to
perform under the agreement or to successfully commercialize our LabCard
products and systems could delay or prevent the commercialization of our
products and result in increased losses.


IF WE ARE UNABLE TO EFFECTIVELY PROTECT OUR INTELLECTUAL PROPERTY, WE WOULD BE
UNABLE TO PREVENT THIRD PARTIES FROM USING OUR TECHNOLOGY, WHICH COULD IMPAIR
OUR ABILITY TO COMPETE IN THE MARKET. THE COST OF ENFORCING OUR PROPRIETARY
RIGHTS MAY BE EXPENSIVE AND RESULT IN INCREASED LOSSES.

    Our success will depend in part on our ability to obtain and maintain
meaningful patent protection for our products, both in the United States and in
other countries, and our inability to do so could harm our competitive position.
We rely on our portfolio of over 120 issued and pending patent applications in
the United States and in other countries to protect a large part of our
intellectual property and our competitive position. We cannot assure you that
any of the currently pending or future patent applications will issue as
patents, or that any patents issued to us will not be challenged, invalidated,
held unenforceable or circumvented. Further, we cannot assure you that our
intellectual property rights will be sufficiently broad to prevent third parties
from producing competing products similar in design to our products.

    In addition to patent protection, we also rely on protection of trade
secrets, know-how and confidential and proprietary information. We generally
enter into confidentiality agreements with our employees, consultants and our
collaborative partners upon commencement of a relationship with us. However, we
cannot assure you that these agreements will provide meaningful protection
against the unauthorized use or disclosure of our trade secrets or other
confidential information or that adequate remedies would exist if unauthorized
use or disclosure were to occur. The exposure of our trade secrets and other
proprietary information would impair our competitive advantages and could have a
material adverse effect on our operating results, financial condition and future
growth prospects. Further, we cannot assure you that others have not or will not
independently develop substantially equivalent know-how and technology.

    Our commercial success also depends in part on avoiding the infringement of
other parties' patents or proprietary rights and the breach of any licenses that
may relate to our technologies and products. We are aware of various third-party
patents that may relate to our technology. We believe that we do not infringe
these patents but cannot assure you that we will not be found in the future to
infringe these or other patents or proprietary rights of third parties, either
with products we are currently developing or with new products that we may seek
to develop in the future. If third parties assert infringement claims against
us, we may be forced to enter into license arrangements with them. We cannot
assure you that we could enter into the required licenses on commercially
reasonable terms, if at all. The failure to obtain necessary licenses or to
implement alternative approaches may prevent us from commercializing products
under development and would impair our ability to be commercially competitive.
We may also become subject to interference proceedings conducted in the U.S.
Patent and Trademark Office to determine the priority of inventions.

    The defense and prosecution, if necessary, of intellectual property suits,
USPTO interference proceedings and related legal and administrative proceedings
will result in substantial expense to us, and significant diversion of effort by
our technical and management personnel. An adverse determination in litigation
or interference proceedings to which we may become a party could subject us to
significant liabilities to third parties, could put our patents at risk of being
invalidated or interpreted narrowly and could put our patent applications at
risk of not issuing.

        Further, there is a risk that some of our confidential information could
be compromised during the discovery process of any litigation. During the course
of any lawsuit, there may be public announcements of the results of hearings,
motions and other interim proceedings or developments in the litigation. If
securities analysts or investors perceive these results to be negative, it could
have a substantial negative effect on the trading price of our stock.


WE ARE INVOLVED IN INTELLECTUAL PROPERTY LITIGATION WITH CALIPER TECHNOLOGIES
CORP. THAT WILL BE EXPENSIVE, MAY HURT OUR COMPETITIVE POSITION, MAY AFFECT OUR
ABILITY TO ENFORCE OUR INTELLECTUAL PROPERTY RIGHTS AND MAY PREVENT US FROM
SELLING CERTAIN OF OUR PRODUCTS.

                                                                         Page 15
<PAGE>   16
    In March 1999, Caliper sued our former patent law firm, an attorney who is
presently our general counsel, and us alleging misappropriation of Caliper's
trade secrets. Caliper claims the attorney and the law firm, who were of counsel
to ACLARA both before and after the alleged events, and who were briefly of
counsel to Caliper during that period, used Caliper's confidential information
in preparing an application for one of our key patents. The attorney joined us
as internal general counsel approximately three years after the alleged events.
The patent in question covers technology used in most of the LabCard chips we
are currently developing. Caliper has asked for unspecified monetary damages and
equitable relief. We believe that Caliper's suit lacks factual and legal merit
and are defending the case vigorously. However, litigation is unpredictable, and
we may not prevail. If we do not prevail, we could owe Caliper a significant
amount of monetary damages. The court could also grant Caliper various forms of
equitable relief including preventing us from enforcing some of our intellectual
property rights against Caliper. As a result, an outcome adverse to us could
cause our business to suffer materially.

    We sued Caliper in April 1999 for infringement of U.S. Patent No. 5,750,015,
or the `015 patent, which covers technology used in most of our current LabCard
chip designs. We believe our case has merit and are pursuing it aggressively.
The court could decide, however, that Caliper does not infringe the `015 patent,
or could find the `015 patent to be invalid or unenforceable. In either case, we
would not be able to prevent Caliper and other third parties from using product
designs that we view as protected by the `015 patent. These outcomes would
reduce the value of our intellectual property rights, weaken our competitive
position and significantly hurt our financial results.

   On July 19 we announced that the U.S. District Court for the Northern
District of California issued a Markman order interpreting the claims of the
`015 patent. Among its rulings, the Court refused to limit the claims to devices
that employed electrophoretic, but not electroosmotic, movement as Caliper had
asserted. The Court held that, in the context of ACLARA's patent, the term
"plurality of electrodes" defines electrodes that are positioned along the axis
of trenches in microfluidic devices, but not necessarily within the trenches
themselves. The Court also determined that the word "trench" as it appears in
the claims of the `015 is defined as an open structure which does not include a
structure that has been permanently covered. In addition, the Court held that
eight of forty-seven claims in the `015 were indefinite and, therefore, invalid.

    In January 2000, Caliper sued us alleging infringement of four patents (U.S.
Patent Nos. 5,858,195, 6,001,229, 6,010,607 and 6,010,608) that they claim to
have licensed exclusively. On March 10, 2000, Caliper amended its lawsuit to
include a fifth patent recently issued, U.S. Patent No. 6,033,546. We believe
our products, which are still under development, do not infringe any claims of
these patents and are defending our position vigorously. In our Answer and
Counter-Claim filed on April 6, 2000, we have denied that we infringe any of
these patents and have further asserted that these patents are invalid and
unenforceable. However, the outcome of any litigation is uncertain, and we may
not prevail. Should we be found to infringe any of these patents, we may be
liable for potential monetary damages, and could be required to obtain a license
from Caliper to commercialize our products or redesign our products so they do
not infringe any of these patents. If we were unable to obtain a license or
adopt a non-infringing product design, we may not be able to proceed with
development, manufacture and sale of some of our products. In this case our
business may not develop as planned, and our results could materially suffer.

    Litigation results are unpredictable. If Caliper prevails on its trade
secret or patent claims or on some or all of its affirmative defenses of
invalidity and unenforceability in the federal action, it could impair our
ability to enforce our intellectual property rights, not just against Caliper
but against other competitors or others using the technology claimed in the `015
and related patents, which could adversely affect our business.

WE HAVE LIMITED MANUFACTURING EXPERIENCE, AND WILL BE SUBJECT TO THE RISK OF
FINALIZING CONTRACTUAL ARRANGEMENTS, TRANSFERRING TECHNOLOGY AND MAINTAINING
RELATIONSHIPS WITH THIRD-PARTY MANUFACTURERS TO MANUFACTURE OUR LABCARD CHIPS.

    We have no experience manufacturing our products in the volumes that will be
necessary for us to achieve significant commercial sales. To date, we have
limited our manufacturing activities to the manufacturing of prototype LabCard
chips for testing purposes and for internal use by our collaborative partners.
The nature of our products requires the use of sophisticated injection molding
and other manufacturing processes that are not widely available. For this reason
only a limited number of vendors currently have the expertise to manufacture our
products. We have relationships with outside suppliers who


                                                                         Page 16
<PAGE>   17


are currently manufacturing limited quantities of our LabCard chips for research
and development purposes. We will need to enter into contractual relationships
with these or other manufacturers for commercial scale production of LabCard
chips and we cannot assure you that we will be able to do so on a timely basis,
for sufficient quantities of chips or on commercially reasonable terms.
Accordingly, we cannot assure you that we can establish or maintain reliable,
high-volume manufacturing at commercially reasonable costs. In addition, the
loss of any of these suppliers may result in a delay or interruption of our
supply of LabCard chips. Any significant delay or interruption would have a
material adverse effect on our ability to supply adequate quantities of our
products and would result in lost revenues.


WE DEPEND ON OUR KEY PERSONNEL, THE LOSS OF WHOM WOULD IMPAIR OUR ABILITY TO
COMPETE.

    Our performance is substantially dependent on the performance of our senior
management and key scientific and technical personnel. We carry key person life
insurance on only two of our senior management personnel. The loss of the
services of any member of our senior management, scientific or technical staff
may significantly delay or prevent the achievement of product development and
other business objectives and could have a material adverse effect on our
business, operating results and financial condition. Our future success will
also depend on the ability to identify, recruit and retain additional qualified
scientific, technical and managerial personnel. There is currently a shortage of
skilled executives and intense competition for such personnel in the areas of
our activities, and we cannot assure you that we will be able to continue to
attract and retain personnel with the advanced qualifications necessary for the
development of our business. The inability to attract and retain the necessary
scientific, technical and managerial personnel could have a material adverse
effect upon our research and development activities, sales revenue, operating
costs and future growth prospects.


WE EXPECT INTENSE COMPETITION IN OUR TARGET MARKETS.

    We compete with companies that design, manufacture and market analytical
instruments for genomics and pharmaceutical drug screening using technologies
such as gel electrophoresis, capillary electrophoresis, microwell plates and
robotic liquid handling systems. In addition, a number of companies are
developing new technologies for miniaturizing various laboratory procedures, for
genomics and drug screening markets targeted by us, using methods such as
hybridization chips and high density microwell plates. Furthermore, we are aware
of other companies that are developing microfluidics technology, including
Caliper Technologies Corp. and Orchid BioSciences, Inc., for potential use in
certain of the markets that we are targeting.

   We anticipate that we will face increased competition in the future as new
companies enter the market with new technologies. Rapidly changing technology,
evolving industry standards, changes in customer needs, emerging competition and
new product introductions characterize the markets for our products. One or more
of our competitors may render our technology obsolete or uneconomical by
advances in existing technological approaches or the development of different
approaches. Many of these competitors have greater financial and personnel
resources and more experience in research and development than we have.
Furthermore, we cannot assure you that the pharmaceutical and biotechnology
companies which are our potential customers or our strategic partners will not
develop competing products.


WE MAY BE SUBJECT TO PRODUCT LIABILITY CLAIMS AND MAY NOT BE ABLE TO OBTAIN
ADEQUATE INSURANCE, WHICH WOULD INCREASE OUR LOSSES IF SUCH CLAIMS OCCURRED.

    Once we have commercially launched our LabCard products, we will face
exposure to product liability claims. Any product liability claims arising in
the future, regardless of their merit or eventual outcome, could increase our
losses. We intend to secure product liability insurance coverage, but we cannot
assure you that we will be able to obtain such insurance on acceptable terms
with adequate coverage, or at reasonable costs. In addition, potential product
liability claims may exceed the amount of our insurance or may be excluded from
coverage under the terms of the policy.

WE MAY BE UNABLE TO RAISE ADDITIONAL CAPITAL WHEN NEEDED OR GENERATE THE CAPITAL
NECESSARY TO EXPAND OUR OPERATIONS AND INVEST IN NEW PRODUCTS, WHICH COULD HURT
OUR ABILITY TO COMPETE OR ACHIEVE PROFITABILITY.


                                                                         Page 17
<PAGE>   18

    It might be necessary for us to raise additional capital over the next few
years to continue our research and development efforts and to commercialize our
products. We believe that the proceeds from our initial public offering and
projected revenue from collaborations should be sufficient to fund our
anticipated levels of operations through at least the end of 2001. However, we
cannot assure you that our business or operations will not change in a manner
that would consume available resources more rapidly than anticipated. We also
cannot assure you that we will continue to receive funding under existing
collaborative arrangements or that existing or potential future collaborations
or sales revenue will be adequate to fund our operations. We may need additional
funds sooner than planned to meet operational needs and capital requirements for
product development and commercialization. We cannot assure you that additional
funds will be available when needed, or on terms acceptable to us, or that
sufficient revenue will be generated from sales. If adequate funds are not
available, we may have to reduce substantially or eliminate expenditures for the
development and production of certain of our proposed products or obtain funds
through arrangements with collaboration partners that require us to relinquish
rights to certain of our technologies or products. Either of these alternatives
could have a material adverse effect on our business, operating results,
financial condition and future growth prospects.


CONCENTRATION OF OWNERSHIP AMONG OUR EXISTING EXECUTIVE OFFICERS, DIRECTORS AND
PRINCIPAL STOCKHOLDERS MAY PREVENT NEW INVESTORS FROM INFLUENCING SIGNIFICANT
CORPORATE DECISIONS.

    Our executive officers, directors and largest stockholders and their
affiliates presently beneficially own or control approximately 44% of the
outstanding shares of common stock, and will until at least 181 days after the
date of the initial public offering. Accordingly, our current executive
officers, directors and their affiliates, if acting together, would have the
ability to control the outcome of corporate actions requiring stockholder
approval, including the election of directors, any merger, consolidation or sale
of all or substantially all of our assets and any other significant corporate
transactions. The concentration of ownership could also delay or prevent a
change of control of our company at a premium price if these stockholders oppose
it.


THE MARKET PRICE OF OUR COMMON STOCK MAY BE HIGHLY VOLATILE.

    There has only been a public market for our common stock since March 21,
2000, and since then our common stock has traded in a range between $20.00 and
$66.00 per share.

    The trading price of our common stock may continue to be highly volatile and
could be subject to wide fluctuations in price in response to various factors,
many of which are beyond our control including: outcome of litigation
proceedings or threatened claims to which we are currently a party; quarterly
fluctuations in results of operations; the company's ability to successfully
commercialize our products; technological innovations or new commercial products
by us or our competitors; developments concerning government regulations or
proprietary rights which could affect the potential growth of our customers; the
execution of new collaborative agreements and material changes in the
relationships with business partners; market reaction to trends in revenues and
expenses, especially research and development; changes in earnings estimates by
analysts; sales of common stock by existing stockholders; and economic and
political conditions. In addition, when the initial public offering lock-up
period expires in September 2000, the price of our common stock may experience
increased volatility.

    The market price for our common stock may also be affected by our ability to
meet analysts' expectations. Any failure to meet such expectations, even
slightly, could have an adverse effect on the market price of the common stock.
In addition, the stock market, and the Nasdaq National Market and the market for
technology companies in particular, is subject to extreme price and volume
fluctuations. This volatility has had a significant effect on the market prices
of securities issued by many companies for reasons unrelated to the operating
performance of these companies. In the past, following periods of volatility in
the market price of a company's securities, securities class action litigation
has often been instituted against the company. If similar litigation were
instituted against us, it could result in substantial costs and a diversion of
our management's attention and resources, which could have an adverse effect on
our business, results of operations and financial condition.


WE HAVE BEEN THREATENED WITH LITIGATION SEEKING RECISSION OF A REPURCHASE OF
SHARES FROM A FORMER STOCKHOLDER, WHICH, IF LITIGATION OCCURS AND IS


                                                                         Page 18
<PAGE>   19



DECIDED ADVERSELY TO ACLARA, COULD RESULT IN SUBSTANTIAL DILUTION TO ALL
STOCKHOLDERS.

In March 1999 we exercised a contractual first right of refusal and repurchased,
at a price of $0.60 per share, 4,521,000 shares of our Series A preferred stock
from 2C Optics, Inc., our former parent company, which was marketing its
position to prospective buyers. In January 2000, after the initial filing of our
S-1 registration statement with the SEC, we received correspondence from an
attorney representing a group of minority shareholders of 2C Optics, including
David Soane, one of our co-founders. This correspondence alleged violations of
corporate and securities laws by us and one or more of our directors, including
our chairman, Thomas Baruch, in connection with our repurchase of these shares,
and that Mr. Baruch, who was a director of both ACLARA and 2C Optics at the time
of the repurchase, violated his fiduciary duties in connection with the
transaction. The correspondence further threatens litigation, based on these
allegations, seeking rescission of the repurchase transaction, unless we allow
each of the attorney's clients to purchase from us, at $0.40 per share, that
number of our shares equal to such client's pro rata interest in the repurchased
shares, based on such client's ownership of 2C Optics. An attorney representing
2C Optics has informed us that they are also considering litigation against us
based on the same allegations. 2C Optics has indicated that they intend to make
a decision in the near future. We have indicated that we believe the claim
against ACLARA and these directors to be without merit and if sued, we will
countersue certain 2C Optics directors for causing any losses incurred by ACLARA
in connection with this matter. We cannot assure you that 2C Optics will not
decide to file a lawsuit against us or seek equitable relief. We believe we have
meritorious defenses to these allegations and, should these persons commence
litigation against us, we will vigorously pursue these defenses. If litigation
is commenced and is decided against us, we may be required to rescind the
repurchase transaction, in whole or in part, which could result in substantial
dilution to our stockholders, or we could be forced to pay monetary damages or
be subjected to further equitable remedies, each of which could result in
increased losses and substantial costs and expenses, thereby affecting our
profitability.

ANTI-TAKEOVER PROVISIONS IN OUR CHARTER DOCUMENTS AND DELAWARE LAW LIMIT THE
ABILITY OF ANOTHER PARTY TO ACQUIRE US, WHICH COULD CAUSE OUR STOCK PRICE TO
DECLINE.

    Certain provisions of our certificate of incorporation and our bylaws could
delay or prevent a third party from acquiring us, even if doing so might be
beneficial to our stockholders. For example, we have a classified board of
directors whose members serve staggered three-year terms and are removable only
for cause. In addition, because we are incorporated in Delaware, we are governed
by the provisions of Section 203 of the Delaware General Corporation Law, which
may prohibit large stockholders from consummating a merger or combination with
us. These provisions could also limit the price that investors might be willing
to pay in the future for our common stock.


                                                                         Page 19
<PAGE>   20

ITEM 3.  QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

    Our exposure to market risk is currently confined to our cash and cash
equivalents which have maturities of less than three months, and our short-term
investments which have average maturities of less than one year. We maintain an
investment portfolio of commercial paper and U.S. government agency bonds. The
securities in our investment portfolio are not leveraged, are classified as
available-for-sale and are, due to their short-term nature, subject to minimal
interest rate risk. We currently do not hedge interest rate exposure. Because of
the short-term maturities of our investments, we do not believe that an increase
in market rates would have any significant negative impact on the realized value
of our investment portfolio but may negatively impact the interest expense
associated with our long-term debt.


                                                                         Page 20
<PAGE>   21

                           PART II. OTHER INFORMATION


ITEM 1.    LEGAL PROCEEDINGS

    Information with respect to this item is incorporated by reference to Note 3
to the condensed consolidated financial statements contained in Part I herein.


                                                                         Page 21
<PAGE>   22

ITEM 2.    CHANGES IN SECURITIES AND USE OF PROCEEDS

    On March 20, 2000, a registration statement on Form S-1 (No. 333-95107) was
declared effective by the Securities and Exchange Commission, pursuant to which
10,350,000 shares of our common stock were offered and sold by us at a price of
$21 per share, generating gross offering proceeds of approximately $217.4
million. The managing underwriters were Deutsche Banc Alex. Brown, Warburg
Dillon Read LLC and U.S. Bancorp Piper Jaffray. In connection with the offering,
we incurred $14.9 million in underwriting discounts and commissions, and
approximately $2.0 million in other related expenses. The net proceeds from the
offering, after deducting the foregoing expenses, were approximately $200.5
million. We have used a portion of the net proceeds of the offering to fund our
continuing research and development activities and for working capital and other
general corporate purposes.

    Employees exercised options to purchase an aggregate of 26,193 shares of our
common stock under our stock option plan in the second quarter of fiscal 2000
for aggregate proceeds to us of $4,547 (with exercise prices ranging from
$0.1083 to $0.40 per share). These issuances were deemed exempt from
registration under the Securities Act of 1933 in reliance upon Rule 701
thereunder.


                                                                         Page 22
<PAGE>   23


ITEM 5.    EXHIBITS AND REPORTS ON FORM 8-K

    (a) Exhibits. The exhibits listed in the accompanying Exhibit Index are
    filed with or incorporated by reference as part of this Report.

    (b) Current Reports on Form 8-K. We did not file any reports on Form 8-K
    during the quarter ended June 30, 2000.


                                                                         Page 23
<PAGE>   24


                                   SIGNATURES


    Pursuant to the requirements 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.



                                   ACLARA BioSciences, Inc.


August 14, 2000                    By: /s/ Joseph M. Limber
                                      -----------------------------------------
                                   Name:  Joseph M. Limber
                                   Title: President and Chief Executive Officer
                                          (Duly Authorized Officer and Acting
                                          Principal Accounting Officer)


                                                                         Page 24
<PAGE>   25


                                  EXHIBIT INDEX
<TABLE>
<CAPTION>

Exhibit                                                                                           Page
Number     Exhibit Title                                                                         Number
-------    ---------------                                                                     ----------

<S>        <C>                                                                                 <C>
3.1        Amended and Restated Certificate of Incorporation of ACLARA BioSciences, Inc. (1)

3.2        Certificate of Amendment to Amended and Restated Certificate of Incorporation of
           ACLARA BioSciences, Inc. (2)

3.3        Amended and Restated Bylaws of ACLARA BioSciences, Inc. (3)

27.1       Financial Data Schedule

(1)        Previously filed as Exhibit 3.3 to our Registration Statement on Form S-1 filed with
           the Securities and Exchange Commission, File No. 333-95107 (our "Form S-1").

(2)        Previously filed as Exhibit 3.6 to our Form S-1.

(3)        Previously filed as Exhibit 3.4 to our Form S-1.
</TABLE>


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