<PAGE>   1

                     U.S. SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549
                                    FORM 10-Q

(Mark one)

[X]  Quarterly report pursuant to Section 13 or 15 (d) of the Securities
     Exchange Act of 1934 for the quarterly period ended September 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:  1-8145


                        THORATEC LABORATORIES CORPORATION
--------------------------------------------------------------------------------
             (Exact name of registrant as specified in its charter)


               California                               94-2340464
------------------------------------------------    --------------------
(State or other jurisdiction of incorporation or     (I.R.S. Employer
             organization)                          Identification No.)

6035 Stoneridge Drive, Pleasanton, California            94588
---------------------------------------------         ----------
  (Address of principal executive offices)            (Zip Code)


Registrant's telephone number, including area code: (925) 847-8600


        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 [ ]


        As of November 10, 2000 registrant had 22,420,975 shares of common stock
outstanding.



<PAGE>   2

                          PART I. FINANCIAL INFORMATION

ITEM 1.  FINANCIAL STATEMENTS

                THORATEC LABORATORIES CORPORATION AND SUBSIDIARY

                      CONDENSED CONSOLIDATED BALANCE SHEETS
                                   (Unaudited)


<TABLE>
<CAPTION>
                                                                  Period End
                                                 ---------------------------------------------

                                                 Fiscal September 2000    Fiscal Year End 1999

                                                 ---------------------    --------------------
<S>                                              <C>                      <C>
ASSETS

Current Assets:

Cash and cash equivalents                              $  5,853,437         $  1,696,522

Short-term investments available-for-sale                12,444,164              276,464

Receivables                                               4,931,223            5,453,187

Inventories (Note 3)                                      8,920,237            6,611,487

Prepaid expenses and other                                  501,061              425,317
                                                       ------------         ------------

Total Current Assets                                     32,650,122           14,462,977

Equipment and Improvements - net                          9,123,751            9,560,814

Other Assets                                              1,063,689            1,036,647
                                                       ------------         ------------

    TOTAL ASSETS                                       $ 42,837,562         $ 25,060,438
                                                       ============         ============


LIABILITIES AND SHAREHOLDERS' EQUITY

Current Liabilities:

Accounts payable                                       $  3,336,000         $  1,703,089

Accrued compensation                                      1,931,536            1,466,147

Deferred distributor revenue (Note 4)                       284,765              284,765

Other                                                       492,729              475,870
                                                       ------------         ------------

    Total Current Liabilities                             6,045,030            3,929,871

Long-term deferred distributor revenue (Note 4)             640,721              854,294
                                                       ------------         ------------

    Total Liabilities                                     6,685,751            4,784,165
                                                       ------------         ------------

Shareholders' Equity:
Common shares,  100,000,000 authorized;
   issued and outstanding  22,418,840 in 2000
   and  20,466,326 in 1999                               89,749,996           72,911,638

Additional capital                                        2,541,223            2,541,223

Accumulated deficit                                     (56,057,967)         (55,191,216)

Accumulated other comprehensive income (loss):

Cumulative translation adjustments                          (81,441)              14,628
                                                       ------------         ------------


Total Shareholders' Equity                               36,151,811           20,276,273
                                                       ------------         ------------

TOTAL LIABILITIES AND SHAREHOLDERS' EQUITY             $ 42,837,562         $ 25,060,438
                                                       ============         ============
</TABLE>

See notes to condensed consolidated financial statements


                                       2
<PAGE>   3

                THORATEC LABORATORIES CORPORATION AND SUBSIDIARY

                 CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS
                                   (Unaudited)


<TABLE>
<CAPTION>
                                          Three Months Ended Fiscal              Nine Months Ended Fiscal
                                                  September                             September
                                       -------------------------------       -------------------------------
                                           2000               1999               2000               1999
                                       ------------       ------------       ------------       ------------
<S>                                    <C>                <C>                <C>                <C>
Product sales                          $  6,194,459       $  5,075,597       $ 21,061,316       $ 15,342,748

Cost of product sales                     2,221,327          2,324,527          7,714,165          6,333,291
                                       ------------       ------------       ------------       ------------

Gross profit                              3,973,132          2,751,070         13,347,151          9,009,457

Operating expenses:
  Research and development                1,808,099          1,451,721          5,286,424          3,882,796
  Selling, general and
    administrative                        2,528,321          2,357,533          7,958,221          6,938,381
  Merger related expenses (Note 8)        1,846,727                 --          1,846,727                 --
                                       ------------       ------------       ------------       ------------
     Total operating expenses             6,183,147          3,809,254         15,091,372         10,821,177
                                       ------------       ------------       ------------       ------------

Other operating income (Note 4)              71,192             71,191            545,177            213,573
                                       ------------       ------------       ------------       ------------

Loss from operations                     (2,138,823)          (986,993)        (1,199,044)        (1,598,147)

Interest and other income - net
(Note 1)                                    272,055             86,073            409,228            315,821

                                       ------------       ------------       ------------       ------------
Loss before taxes                        (1,866,768)          (900,920)          (789,816)        (1,282,326)

Income tax expense (Note 7)                   2,487              1,334             76,935              8,440
                                       ------------       ------------       ------------       ------------

Net loss                               $ (1,869,255)      $   (902,254)      $   (866,751)      $ (1,290,766)
                                       ============       ============       ============       ============

Loss per share: (Note 6)
   Basic and Diluted                   $      (0.08)      $      (0.04)      $      (0.04)      $      (0.06)

Shares used to compute loss per
  share: (Note 6)
   Basic and Diluted                     22,386,921         20,455,018         21,634,134         20,439,394
</TABLE>

See notes to condensed consolidated financial statements.


                                       3
<PAGE>   4

                THORATEC LABORATORIES CORPORATION AND SUBSIDIARY
                 CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS
                                   (Unaudited)

<TABLE>
<CAPTION>
                                                            Nine Months Ended Fiscal September
                                                            ----------------------------------
                                                                2000               1999
                                                            ------------       ------------
<S>                                                         <C>                <C>
Cash flows from operating activities:
     Net loss                                               $   (866,751)      $ (1,290,766)

     Adjustments to reconcile net income (loss) to net
       cash used in operating activities:
       Amortization of deferred distributor revenue             (213,573)          (213,573)
       Common stock options granted for services                                     45,244
       Loss on disposal of capital assets                         66,312              2,034
       Depreciation and amortization                             978,951            761,512
       Changes in assets and liabilities:
             Receivables                                         408,153           (410,666)
             Prepaid expenses and other                          (77,431)           103,628
             Inventories                                      (2,394,752)        (1,762,145)
             Other assets                                        (27,443)           779,428
             Accounts payable and other liabilities            2,233,863           (282,406)
             Deferred distributor revenue                             --          1,423,823
                                                            ------------       ------------

             Net cash provided by (used in) operating
             activities                                          107,329           (843,887)
                                                            ------------       ------------

Cash flows from investing activities:
    Purchases of short-term investments
       available-for-sale                                    (58,795,849)        (6,723,256)
    Maturities of short-term investments
       available-for-sale                                     46,343,934          5,284,000
    Sales of short-term investments available-for-sale           284,215          1,349,272
    Capital expenditures                                        (622,233)          (543,601)
                                                            ------------       ------------

            Net cash used in investing activities            (12,789,933)          (633,585)
                                                            ------------       ------------

Cash flows from financing activities:
    Net proceeds from public offering of common stock         15,708,056                 --
    Common stock issued upon exercise of options               1,172,802             98,567
                                                            ------------       ------------
            Net cash provided by financing activities         16,880,858             98,567
                                                            ------------       ------------

Effect of exchange rate changes on cash                          (41,339)           (18,905)
                                                            ------------       ------------

Net increase (decrease) in cash and cash equivalents           4,156,915         (1,397,810)

Cash and cash equivalents at beginning of period               1,696,522          2,712,686
                                                            ------------       ------------

Cash and cash equivalents at end of period                  $  5,853,437       $  1,314,876
                                                            ============       ============

Noncash Investing Transaction:
     Capital assets in accounts payable                     $     83,806       $     67,078


Noncash Financing Transaction:
     Deferred financing charges in accounts payable         $     42,500                 --
</TABLE>


See notes to condensed consolidated financial statements.


                                       4
<PAGE>   5

                THORATEC LABORATORIES CORPORATION AND SUBSIDIARY
             CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE LOSS
                                   (Unaudited)


<TABLE>
<CAPTION>
                                                        Three Months Ended                   Nine Months Ended
                                                         Fiscal September                     Fiscal September
                                                    -----------------------------       -----------------------------
                                                        2000              1999              2000              1999
                                                    -----------       -----------       -----------       -----------
<S>                                                 <C>               <C>               <C>               <C>
Net loss                                            $(1,869,255)      $  (902,254)      $  (866,751)      $(1,290,766)
  Other net comprehensive income:
    Unrealized gain (loss) on securities                     --               585                --            (1,953)
    Foreign currency translation adjustments            (66,505)          183,592           (96,069)          (45,787)
                                                    -----------       -----------       -----------       -----------
  Comprehensive loss                                $(1,935,760)      $  (718,077)      $  (962,820)      $(1,338,506)
                                                    ===========       ===========       ===========       ===========
</TABLE>


See notes to condensed consolidated financial statements.


                                       5
<PAGE>   6

                THORATEC LABORATORIES CORPORATION AND SUBSIDIARY

              NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS
                                   (Unaudited)


1.      BASIS OF PRESENTATION

        The interim condensed consolidated financial statements presented have
        been prepared by us without audit and, in our opinion, reflect all
        adjustments necessary (consisting only of normal recurring adjustments)
        to present fairly the financial position, results of operations and cash
        flows at September 30, 2000 (third quarter 2000) and for the three and
        nine-month periods ended September 30, 2000 (third quarter and first
        nine months of 2000) and the three and nine-month periods ended October
        2, 1999 (third quarter and first nine months of 1999). The results of
        operations for any interim period are not necessarily indicative of
        results for a full year.

        The condensed consolidated balance sheet presented as of the end of
        1999 (January 1, 2000) has been derived from the condensed consolidated
        financial statements that have been audited by our independent public
        accountants. The consolidated financial statements and notes are
        presented as permitted by the Securities and Exchange Commission and
        do not contain certain information included in our annual consolidated
        financial statements and notes. We suggest that the accompanying
        condensed consolidated financial statements be read in conjunction with
        the audited consolidated financial statements and the notes thereto
        contained in our Annual Report on Form 10-K for the 1999 fiscal year,
        which have been filed with the Securities and Exchange Commission.

        The preparation of our consolidated financial statements in conformity
        with generally accepted accounting principles necessarily requires us to
        make estimates and assumptions that affect the reported amounts of
        assets and liabilities and disclosure of contingent assets and
        liabilities at the consolidated balance sheet dates and the reported
        amounts of revenues and expenses for the periods presented.

        All assets and liabilities of our non-United States operations are
        translated into United States dollars at the fiscal period-end exchange
        rates, and, except as follows, the resulting translation adjustments are
        included in comprehensive income. Exchange rate fluctuations resulting
        from the period-end translation of the current portion of the
        intercompany obligation of our wholly owned subsidiary into United
        States dollars are recorded in the income statement as foreign currency
        exchange gains or losses and are included in interest and other income.
        Net foreign currency exchange loss was approximately $68,000 in the
        third quarter 2000, approximately $269,000 in the first nine months of
        2000, and zero for both the third quarter 1999 and the first nine months
        of 1999.

        The calculation of diluted EPS takes into account the effect of dilutive
        instruments, such as stock options and warrants, and uses the average
        share price for the period in determining the number of incremental
        shares that are to be added to the weighted average number of shares
        outstanding. Diluted EPS for all periods presented excludes the effect
        of any such instruments, as their inclusion would be anti-dilutive.

        We have made certain reclassifications to the 1999 amounts to conform to
        the 2000 presentation.


                                       6
<PAGE>   7

2.      RECENTLY ISSUED ACCOUNTING STANDARDS

        During June 1998, the Financial Accounting Standards Board (FASB) issued
        Statement of Financial Accounting Standards No. 133, "Accounting for
        Derivative Instruments and Hedging Activities", which defines
        derivatives, requires that all derivatives be carried at fair value, and
        provides for hedge accounting when certain conditions are met. Such
        Statement is effective for all fiscal quarters of fiscal years beginning
        after June 15, 2000. We will implement this standard in the fiscal year
        beginning December 31, 2000. We have not yet completed our evaluation
        of the impact of the adoption of the new standard, however, we do not
        expect that this will have a material impact on our financial
        statements.

        In December 1999 the Securities and Exchange Commission released Staff
        Accounting Bulletin No. 101 "Revenue Recognition in Financial
        Statements" which summarizes certain of the staff's views in applying
        generally accepted accounting principles to revenue recognition in
        financial statements. In addition, on October 13, 2000, the SEC issued a
        Frequently Asked Questions ("FAQ") document which clarified and
        elaborated the SEC staff's views regarding revenue recognition. We will
        adopt this statement in the fourth fiscal quarter of our fiscal year
        ending December 30, 2000. We do not expect any material impact as a
        result of adopting the guidelines of this standard.

        In March 2000, the Financial Accounting Standards Board issued
        Interpretation No. 44, Accounting for Certain Transactions Involving
        Stock Compensation (FIN 44), that clarifies guidance for certain issues
        related to the application of APB Opinion No. 25, Accounting for Stock
        Issued to Employees (APB 25). Such statement is effective for all new
        awards and modifications after June 30, 2000. The implementation of this
        standard has not resulted in any material impact to our financial
        records.


3.      INVENTORIES


        Inventories consist of the following:

<TABLE>
<CAPTION>
                                                  Period Ended
                                       -----------------------------------
                                       Third Quarter 2000    Year End 1999
                                       ------------------    -------------
<S>                                    <C>                   <C>
        Finished goods                     $5,402,676          $3,163,055

        Work in process                     1,863,182           2,033,194

        Raw materials                       1,654,379           1,415,238
                                           ----------          ----------

        Total                              $8,920,237          $6,611,487
                                           ==========          ==========
</TABLE>



                                       7
<PAGE>   8

4.      LICENSE AGREEMENT AND DISTRIBUTION AGREEMENT

        In the first quarter of 2000, we amended the license granted to Gambro,
        Inc., formerly known as COBE Laboratories, Inc., to be a fully paid-up,
        world-wide, irrevocable field-of-use license and sublicense (with the
        right to sublicense others) for our biomaterials to be used in some of
        Gambro's products. The original license was granted in 1992 and was for
        use in renal dialysis devices, blood component devices and blood tubing
        sets and accessories used in direct connection with any of these. We
        received a one-time payment of approximately $330,000 in the first
        quarter of 2000 in conjunction with this amendment, which is included in
        other operating income in the first quarter of 2000. Thoratec has no
        continuing obligation to Gambro under this license agreement.

        During the first quarter of 1999, we entered into a five-year
        distribution agreement with Guidant Corporation. Under the terms of the
        agreement, Guidant receives exclusive worldwide marketing and
        distribution rights to our Vectra(TM) vascular access graft product
        line, except in Japan. In exchange for these rights, Guidant made a $1.5
        million non-refundable payment in the first quarter of 1999, and will
        pay up to an additional $2 million when the Vectra product line receives
        FDA approval for use in the United States. In the first quarter of 1999,
        we began recognizing the $1.5 million contract payment ratably over the
        five-year life of the contract. Other operating income in 2000 and 1999
        include approximately $71,000 of such payment amortization in each of
        the first three quarters.


5.      PUBLIC OFFERING

        In April 2000, we sold, through an underwritten public offering,
        2,000,000 shares of common stock at $10.00 per share. Included in the
        2,000,000 shares were 500,000 shares offered by Gambro Inc., a major
        shareholder of our company, for which we received no proceeds. In
        addition, the underwriters exercised a 30-day option to purchase from us
        and Gambro 300,000 shares of common stock to cover any over-allotments,
        of which the proceeds from 225,000 shares were received by us. After
        deducting underwriting discounts of approximately $983,000, we received
        a total of $16,267,000, from which approximately $600,000 in
        offering-related costs have been paid. Underwriting discounts and the
        other estimated offering-related costs were recorded as an offset to
        common stock at the closing of the offering. We intend to use the net
        proceeds for clinical trials of products under development, expansion of
        our sales and marketing capabilities, research and development,
        potential acquisitions of complementary technology, working capital and
        other general corporate purposes.




                                       8
<PAGE>   9

6.      LOSS PER SHARE

        Basic earnings per share are computed by dividing net loss by the
        weighted average number of common shares outstanding during the period.
        Diluted earnings per share reflect the potential dilution that could
        occur if securities or other contracts to issue common stock were
        exercised or converted into common stock. Diluted earnings per share for
        all periods presented exclude any effect from such securities as their
        inclusion would be antidilutive, therefore, diluted earnings per share
        is the same as basic earnings per share for all periods presented.

        Basic and diluted loss per share were calculated as follows:


<TABLE>
<CAPTION>
                                               Three Months Ended                    Nine Months Ended
                                       ---------------------------------     ---------------------------------
                                       September 2000     September 1999     September 2000     September 1999
                                       --------------     --------------     --------------     --------------
<S>                                    <C>                <C>                <C>                <C>
        Net loss                        $ (1,869,255)      $   (902,254)      $   (866,751)      $ (1,290,766)

        Weighted average common
        shares outstanding - basic
        and diluted                       22,386,891         20,455,018         21,634,124         20,439,394
        Basic and diluted loss per
        common share                    $      (0.08)      $      (0.04)      $      (0.04)      $      (0.06)
</TABLE>


7.      INCOME TAXES

        The provision for income taxes was approximately $2,500 and $77,000 for
        the three and nine-month periods ended fiscal September 2000 and
        represents federal alternative minimum, state and local taxes. The
        provision for income taxes was approximately $1,300 and $8,400 for the
        three and nine-month periods ended fiscal September 1999 and represents
        state and local taxes.

8.      SUBSEQUENT EVENT

        On October 3, 2000 we signed a definitive agreement to acquire Thermo
        Cardiosystems, a Massachusetts-based manufacturer of cardiac assist,
        blood coagulation and skin incision devices. The transaction is a
        stock-for-stock transaction, accounted for as a reverse acquisition
        purchase in which Thermo Cardiosystem is treated as the acquirer of
        Thoratec for financial reporting purposes, and will be
        treated as a tax-free exchange. Under the terms of the agreement, each
        outstanding share of Thermo Cardiosystems stock will be exchanged for
        0.835 shares of newly issued Thoratec stock. Following completion of the
        transaction, current Thoratec shareholders will own approximately 43
        percent of the proforma shares outstanding. Thermo Electron Corporation,
        the parent company of Thermo Cardiosystems, will receive shares
        representing approximately 34 percent of the proforma shares
        outstanding, which will be subject to certain contractual lock-up
        provisions. Completion of the merger transaction is subject to approval
        by the shareholders of Thoratec, the shareholders of Thermo
        Cardiosystems, and certain governmental regulatory agencies. If such
        approvals are not received by March 1, 2001, either party may withdraw
        from the agreement without penalty.


                                       9
<PAGE>   10

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

Liquidity and Capital Resources

At the end of September 2000 we had working capital of $26.6 million compared
with $10.5 million at the end of 1999. Cash, cash equivalents, and short-term
investments available for sale increased $16.3 million to $18.3 million
principally due to net proceeds received from our April 2000 public sale of
common stock of $15.7 million, a $350,000 license payment from Gambro, Inc.,
discussed below, and $1.2 million from stock option exercises, less capital
expenditures of $622,000. Accounts receivable decreased due to lower product
sales in the third quarter 2000 as compared to the fourth quarter of 1999.
Inventories increased $2.3 million to $8.9 million due to lower than expected
sales in the quarter in addition to preparation for planned increases in product
sales and a higher number of units available for our rent-to-own program.
Current liabilities increased $2.1 million to $6.0 million, principally from
liabilities incurred to outside consultants related to our planned merger with
Thermo CardioSystems Inc., discussed below.

In the first quarter of 2000, we amended the license granted to Gambro, Inc.,
formerly known as COBE Laboratories, Inc., to be a fully paid-up, world-wide,
irrevocable field-of-use license and sublicense (with the right to sublicense
others) for our biomaterials to be used in some of Gambro's products. The
original license was granted in 1992 and was for use in renal dialysis devices,
blood component devices and blood tubing sets and accessories used in direct
connection with any of these. We received a one-time payment of approximately
$330,000 in the first quarter of 2000 in conjunction with this amendment, which
is included in other operating income in the first quarter of 2000. Thoratec has
no continuing obligation to Gambro under this license agreement.

In April 2000, we sold, through an underwritten public offering, 2,000,000
shares of common stock at $10.00 per share. Included in the 2,000,000 shares
were 500,000 shares offered by Gambro Inc., a major shareholder of our company,
for which we received no proceeds. In addition, the underwriters exercised a
30-day option to purchase from us and Gambro 300,000 shares of common stock to
cover over-allotments, of which the proceeds from 225,000 shares were received
by us. After deducting underwriting discounts of approximately $983,000, we
received a total of $16,267,000, from which approximately $600,000 in
offering-related costs have been paid. Underwriting discounts and the other
estimated offering-related costs were recorded as an offset to common stock at
the closing of the offering.

On October 3, 2000 we signed a definitive agreement to acquire Thermo
Cardiosystems, a Massachusetts-based manufacturer of cardiac assist, blood
coagulation and skin incision devices. The transaction is a stock-for-stock
transaction, accounted for as a reverse acquisition purchase in which Thermo
Cardiosystems is treated as the acquirer of Thoretec for financial reporting
purposes, and will be treated as a tax-free exchange. Under the terms of the
agreement, each outstanding share of Thermo Cardiosystems stock will be
exchanged for 0.835 shares of newly issued Thoratec stock. Following completion
of the transaction, current Thoratec shareholders will own approximately 43
percent of the proforma shares outstanding. Thermo Electron Corporation, the
parent company of Thermo Cardiosystems, will receive shares representing
approximately 34 percent of the proforma shares outstanding, which will be
subject to certain contractual lock-up provisions. Completion of the merger
transaction is subject to approval by the shareholders of Thoratec, the
shareholders of Thermo Cardiosystems, and certain governmental regulatory
agencies. If such approvals are not received by March 1, 2001, either party may
withdraw from the agreement without penalty.


                                       10
<PAGE>   11

We believe that expected cash flow from operations, in conjunction with the
proceeds of the public offering, will be sufficient to fund our operations for
at least the next twelve months. We expect that our operating expenses will
increase in future periods as we spend more on product manufacturing, marketing
and research and development of new product lines as well as substantial costs
associated with completing the merger transaction with Thermo Cardiosystems.

We do not expect that inflation will have a material impact on our operations.





                                       11
<PAGE>   12

Results of Operations

Third quarter 2000 and 1999

Product sales in the third quarter of 2000 were $6.2 million compared to $5.1
million in the third quarter of 1999, an increase of approximately $1.1 million
or 22%. The increase is attributable to sales of our VAD System disposable blood
pumps and cannulae, which increased to approximately $5.2 million in the third
quarter of 2000 from $4.2 million in the third quarter of 1999, an increase of
approximately $1.0 million or 24%. The growth of sales in VAD disposables was
primarily attributable to a 19% increase in the average selling prices of our
VAD pump, and an increase in the number VAD pumps sold. The total number of
centers using our VAD System increased to 155 at the end of the third quarter of
2000 from 117 at the end of the third quarter of 1999.

Gross profit was $4.0 million, representing approximately 64% of product sales
for the third quarter of 2000 compared to a gross profit of $2.8 million
representing approximately 54% of product sales for the third quarter of 1999.
The increase in gross profit percentage was due to higher average selling prices
for the VAD pumps in addition to a higher proportion of VAD System disposables
being sold in the United States in the third quarter of 2000 compared to the
third quarter of 1999. VAD disposable products sold in the United States
generally have a higher gross margin than those sold in the rest of the world.

Research and development expenses were approximately 29% of product sales in the
third quarters of both 2000 and 1999. These expenses increased to $1.8 million
in the third quarter of 2000 from $1.5 million in the third quarter of 1999, an
increase of $356,000, or 25%. Of the total increase in research and development
expenses, $161,000 was due to continued development activities for our TLC-II
portable driver, and $120,000 was due to indirect engineering and manufacturing
expenses, representing higher overall facilities expenses and higher levels of
support from quality assurance and manufacturing personnel.

Selling, general and administrative expenses increased to $2.5 million in the
third quarter of 2000, from $2.4 million in the third quarter of 1999, an
increase of $171,000 or 7%. As a percent of sales, these expenses decreased from
46% of sales in third quarter 1999 to 41% of sales in third quarter 2000. The
increase is due to $367,000 higher selling and marketing expenses associated
with the continued development of the domestic and European sales organizations
and other promotional activities, partially offset by lower consulting and legal
expenses.

Merger related expenses were $1.8 million and were comprised of external costs
associated directly with the merger transaction. These costs are principally
related to outside consulting, accounting, and legal expenses. Net income in the
third quarter of 2000, exclusive of merger costs, would have been approximately
$23,000 or $0.00 per share.

Interest and other income in the third quarter of 2000 increased from the third
quarter of 1999, with $261,000 higher interest income resulting from higher cash
balances offset by $68,000 of foreign currency exchange losses.


                                       12
<PAGE>   13

Nine months ended September 2000 and September 1999

Product sales for the nine-month period ended September 2000 were $21.1 million
compared to $15.3 million for the nine-month period ended September 1999, an
increase of approximately $5.7 million or 37%. The increase is attributable to
sales of our VAD System disposable blood pumps and cannulae, which increased to
approximately $18.1 million in the nine-month period ended September 2000 from
$12.4 million in the nine-month period ended September 1999, an increase of
approximately $5.7 million or 46%. The growth of sales in VAD disposables was
primarily attributable to a 36% increase in the number of VAD pumps sold. An
increase in the average selling price of our domestic VAD pumps also contributed
to the increase in revenue as compared to the same nine-month period of last
year.

Gross profit was $13.3 million, representing approximately 63% of product sales
for the nine-month period ended September 2000 compared to a gross profit of
$9.0 million representing approximately 59% of product sales for the nine-month
period ended September 1999. The increase in gross profit percentage was due to
a higher average selling price for our domestic VAD pump and a higher proportion
of VAD System disposables being sold in the United States in the nine-month
period ended September 2000 as compared to the nine-month period ended September
1999. VAD disposable products sold in the United States generally have a higher
gross margin than those sold in the rest of the world because the average
selling price of VAD pumps sold in the United States is higher. Partially
offsetting the favorable geographic sales mix and higher domestic average
selling prices for the VAD System disposables was approximately $423,000 in
higher manufacturing, service and retrofitting costs associated with a change in
a component used in our TLC-II portable driver.

Research and development expenses increased to $5.3 million in the nine-month
period ended September 2000, from $3.9 million in the nine-month period ended
September 1999, an increase of $1.4 million or 36%, representing 25% of product
sales for both 2000 and 1999. Of the total increase in research and development
expenses, $197,000 was due to increased research spending for the implantable
version of our ventricular assist device, $213,000 was due to graft products,
$433,000 was due to the TLC-II, and $497,000 was due to indirect engineering and
manufacturing expenses, representing higher overall facilities expenses and
higher levels of support from quality assurance and manufacturing personnel.

Selling, general and administrative expenses increased to $8.0 million in the
nine-month period ended September 2000, representing 38% of sales, from $6.9
million in the nine-month period ended September 1999, representing 45% of
sales, an increase of $1.0 million or 15%. Of the total increase in selling,
general, and administrative expenses, $945,000 is associated with the continued
development of the domestic and European sales organizations and other
promotional activities, and $75,000 is associated with various administrative
expenses, principally related to increased personnel expenses and higher
expenses related to our annual report to shareholders and other year-end
statutory reports.

Merger related expenses were $1.8 million and were comprised of external costs
associated directly with the merger transaction. These costs are principally
related to outside consulting, accounting, and legal expenses. Net income in the
first nine months of 2000, exclusive of merger costs, would have been
approximately $980,000, or $0.05 per share.

Interest and other income in the nine-month period ended September 2000
increased $93,000 from the nine-month period ended September 1999 and was
principally due to $401,000 higher interest income resulting from higher cash
balances partially offset by $269,000 of foreign exchange losses and $48,000 of
lower grant revenue.


                                       13
<PAGE>   14

Forward-Looking Statements

The statements in this report that relate to future plans, events or performance
are forward-looking statements which involve risks and uncertainties. These
risks include those related to our proposed transaction with Thermo
Cardiosystems, the results of clinical trials, government regulatory approval
processes, delays in product development and new product introductions,
announcements by our competitors, an intensely competitive market, and market
acceptance of new products. Completion of the merger transaction is subject to
approval by the shareholders of Thoratec, the Shareholders of Thermo
Cardiosystems, and certain governmental and other regulatory agencies. If such
approvals are not received by March 1, 2001, either party may withdraw from the
agreement without penalty. There can be no assurance that we will receive all
necessary approvals before the date specified in the merger agreement, it at
all.

These factors, and others, are discussed more fully in our annual report on Form
10-K for 1999 and our other filings with the Securities and Exchange Commission.
Actual results, events or performance may differ materially. These
forward-looking statements speak only as of the date hereof.

We undertake no obligation to publicly release the result of any revisions to
these forward-looking statements that may be needed to reflect events or
circumstances after the date hereof or to reflect the occurrence of
unanticipated events.


ITEM 3. QUANTITATIVE AND QUALITATIVE DISCLOSURE OF MARKET RISK

We do not currently use derivative financial instruments in our operations or
investment portfolio. We do not have material exposure to market risk associated
with changes in interest rates as we have no long-term debt obligations or
long-term investments outstanding. Our investment portfolio at the end of 1999
consisted of short-term corporate debt instruments and Federal government agency
debt instruments that were classified as available-for-sale. The weighted
average maturity of our investment portfolio was less than 90 days in 1999. Our
investment portfolio at the end of the third quarter of 2000 had a weighted
average maturity of 14 days and consisted primarily of state and municipal
government bonds. We do not expect to be subject to material interest rate risk
with respect to our short-term investments. We do not believe we have any other
material exposure to market risk associated with interest rates.

We conduct business in foreign countries. Our international operations consist
primarily of sales and service personnel for our VAD System. These employees
report into our U.S. sales and marketing group and are internally reported as
part of that group. All assets and liabilities of our non-United States
operations are translated into United States dollars at the fiscal period-end
exchange rates, and, except as follows, the resulting translation adjustments
are included in comprehensive income. Exchange rate fluctuations resulting from
the period-end translation of the current portion of the intercompany obligation
of our wholly owned subsidiary into United States dollars are recorded in the
income statement as foreign currency exchange gains or losses and are included
in interest and other income. Net foreign currency exchange loss was
approximately $68,000 in the third quarter 2000, approximately $269,000 in the
first nine months of 2000, and zero for both the third quarter 1999 and the
first nine months of 1999.

Although we do not expect to be subject to material foreign currency risk with
respect to future costs or cash flows from our foreign operations, to date, we
have not entered into any significant foreign currency forward exchange
contracts or other derivative financial instruments to hedge the effects of
adverse fluctuations in foreign currency exchange.


                                       14
<PAGE>   15

PART II. OTHER INFORMATION


ITEM 6. EXHIBITS AND REPORTS ON FORM 8-K

        (a)    Exhibits required by Item 601 of Regulation S-K

               See Exhibit Index on the page immediately preceding exhibits.

        (b)    Reports on Form 8-K

               No reports on Form 8-K were filed during the quarter.





                                       15

<PAGE>   16

                                   SIGNATURES


In accordance with the requirements of the Exchange Act, the registrant caused
this report to be signed on its behalf by the undersigned, thereunto duly
authorized.




                                      THORATEC LABORATORIES CORPORATION


Date: November 13, 2000                       /s/ D. Keith Grossman
      -------------------         ----------------------------------------------
                                      D. Keith Grossman, Chief Executive Officer


Date: November 13, 2000                        /s/ Cheryl D. Hess
      -------------------         ----------------------------------------------
                                        Cheryl D. Hess, Chief Financial Officer





                                       16
<PAGE>   17

                                  EXHIBIT INDEX



   Exhibit Number                              Document
   --------------                              --------

         27                            Financial Data Schedule







                                       17