<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 October 2, 1999 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 Small Business Issuer 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 3, 1999 registrant had 20,465,203 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>
                                                     October 2, 1999      January 2, 1999
                                                     ---------------      ---------------
<S>                                                  <C>                  <C>
ASSETS

Current Assets:
Cash and cash equivalents                              $  1,314,876         $  2,712,686
Short-term investments available-for-sale                 2,120,138            2,032,107
Receivables                                               3,746,327            4,141,854
Inventories (Note 3)                                      7,046,487            5,290,745
Prepaid expenses and other                                  300,588              404,737
                                                       ------------         ------------
Total Current Assets                                     14,528,416           14,582,129
Equipment and improvements, at cost                      11,810,989           12,460,755
Accumulated depreciation and amortization                (2,417,084)          (2,835,365)
                                                       ------------         ------------
Equipment and leasehold improvements - net                9,393,905            9,625,390
Other Assets                                              1,027,161            1,000,898
                                                       ------------         ------------
TOTAL ASSETS                                           $ 24,949,482         $ 25,208,417
                                                       ============         ============

LIABILITIES AND SHAREHOLDERS' EQUITY

Current Liabilities:
Accounts payable                                       $  1,126,467         $  1,307,768
Accrued compensation                                      1,385,453            1,613,334
Deferred distributor revenue (Note 5)                       284,765
Other                                                       544,650              409,958
                                                       ------------         ------------
Total Current Liabilities                                 3,341,335            3,331,060
Long-term deferred distributor revenue (Note 5)             925,485
                                                       ------------         ------------
Total liabilities                                         4,266,820            3,331,060
                                                       ------------         ------------
Shareholders' Equity:
Common shares, 100,000,000 authorized;
   issued and outstanding 20,459,743 in 1999
   and 20,422,952 in 1998                                72,909,017           72,810,450
Paid-in capital                                           2,527,473            2,482,229
Accumulated deficit                                     (54,692,872)         (53,402,106)
Other comprehensive loss:
Unrealized loss on investments - net                         (1,945)                   8
Cumulative translation adjustments                          (59,011)             (13,224)
                                                       ------------         ------------
Total other comprehensive loss                              (60,956)             (13,216)
                                                       ------------         ------------
Total Shareholders' Equity                               20,682,662           21,877,357
                                                       ------------         ------------
TOTAL LIABILITIES AND SHAREHOLDERS' EQUITY             $ 24,949,482         $ 25,208,417
                                                       ============         ============
</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                        Nine Months Ended
                                                  ---------------------------------         ---------------------------------
                                                   October 2,           October 3,           October 2,           October 3,
                                                      1999                 1998                 1999                 1998
                                                  ------------         ------------         ------------         ------------
<S>                                               <C>                  <C>                  <C>                  <C>
Revenue:
  Product sales - net                             $  5,075,597         $  3,618,193         $ 15,342,748         $ 11,329,653
  Interest and other income                            157,264              129,156              529,492              524,569
                                                  ------------         ------------         ------------         ------------
  Total revenue                                      5,232,861            3,747,349           15,872,240           11,854,222
                                                  ------------         ------------         ------------         ------------
Costs and expenses:
  Costs of products sold                             2,324,527            1,480,101            6,333,291            4,457,804
  Research and development                           1,451,721            1,207,110            3,882,796            3,692,604
  Selling, general and administrative                2,358,867            1,678,449            6,946,919            5,566,433
                                                  ------------         ------------         ------------         ------------
  Total costs and expenses                           6,135,115            4,365,660           17,163,006           13,716,841
                                                  ------------         ------------         ------------         ------------
Net loss                                          $   (902,254)        $   (618,311)        $ (1,290,766)        $ (1,862,619)
                                                  ============         ============         ============         ============
 Basic and diluted loss per share (Note 4)        $      (0.04)        $      (0.03)        $      (0.06)        $      (0.09)
                                                  ============         ============         ============         ============
  Shares used to compute basic and
     diluted loss per share                         20,455,018           20,355,375           20,439,394           20,320,976
</TABLE>


See notes to condensed consolidated financial statements.


                                       3
<PAGE>   4
                THORATEC LABORATORIES CORPORATION AND SUBSIDIARY

             CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE LOSS
                                   (Unaudited)



<TABLE>
<CAPTION>
                                                           Three Months Ended                      Nine Months Ended
                                                    --------------------------------        --------------------------------
                                                     October 2,          October 3,          October 2,          October 3,
                                                        1999                1998                1999                1998
                                                    ------------        ------------        ------------        ------------
<S>                                                 <C>                 <C>                 <C>                 <C>
Net loss                                            $   (902,254)       $   (618,311)       $ (1,290,766)       $ (1,862,619)
Other net comprehensive income:
    Unrealized gain (loss) on securities                     585               1,822              (1,953)              8,659
    Foreign currency translation adjustments             183,592              37,436             (45,787)             44,778
                                                    ------------        ------------        ------------        ------------
Other comprehensive income (loss)                        184,177              39,258             (47,740)             53,437
                                                    ------------        ------------        ------------        ------------
Comprehensive loss                                  $   (718,077)       $   (579,053)       $ (1,338,506)       $ (1,809,182)
                                                    ============        ============        ============        ============
</TABLE>


See notes to condensed consolidated financial statements.


                                       4
<PAGE>   5
                THORATEC LABORATORIES CORPORATION AND SUBSIDIARY

                 CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS
                                   (Unaudited)


<TABLE>
<CAPTION>
                                                                                  Nine Months Ended
                                                                         ------------------------------------
                                                                         October 2, 1999      October 3, 1998
                                                                         ---------------      ---------------
<S>                                                                      <C>                  <C>
Cash flows from operating activities:
     Net loss                                                             $ (1,290,766)        $ (1,862,619)
     Adjustments to reconcile net loss to net cash used in
     operating activities:
       Amortization of deferred distributor revenue                           (213,573)
       Common stock options granted for services                                45,244
       Depreciation and amortization                                           763,546              500,501
       Changes in assets and liabilities:
             Receivables                                                       395,086           (1,433,228)
             Prepaid expenses and other                                        103,628               21,484
             Inventories                                                    (1,762,145)          (1,845,891)
             Other Assets                                                      (26,324)             (47,108)
             Accounts payable and other liabilities                           (282,406)             187,076
             Deferred distributor revenue                                    1,423,823
                                                                          ------------         ------------

Net cash used in operating activities                                         (843,887)          (4,479,785)
                                                                          ------------         ------------

Cash flows from investing activities:
    Purchases of short-term investments available-for-sale                  (6,723,256)         (12,465,364)
    Maturities of short-term investments available-for-sale                  5,284,000           14,875,000
    Sales of short-term investments available-for-sale                       1,349,272              382,028
    Capital expenditures                                                      (543,601)          (4,530,270)
                                                                          ------------         ------------

         Net cash provided by (used in) investing activities                  (633,585)          (1,738,606)
                                                                          ------------         ------------

Cash flows from financing activities:
    Common stock issued upon exercise of options                                98,567               90,833
                                                                          ------------         ------------

         Net cash provided by financing activities                              98,567               90,833
                                                                          ------------         ------------

Effect of exchange rate changes on cash                                        (18,905)              12,066
                                                                          ------------         ------------

Net increase (decrease) in cash and cash equivalents                        (1,397,810)          (6,115,492)

Cash and cash equivalents at beginning of period                             2,712,686            9,469,311
                                                                          ------------         ------------

Cash and cash equivalents at end of period                                $  1,314,876         $  3,353,819
                                                                          ============         ============

Noncash Financing Transaction:
         Construction costs and capital assets in accounts payable        $     67,078         $    417,561
</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 consolidated financial statements presented have been
        prepared by Thoratec Laboratories Corporation (the Company) without
        audit and, in the opinion of management, reflect all adjustments
        necessary (consisting only of normal recurring adjustments) to present
        fairly the financial position, results of operations and cash flows at
        October 2, 1999 and for all periods presented. The results of operations
        for any interim period are not necessarily indicative of results for a
        full year.

        The consolidated balance sheet presented as of January 2, 1999, has been
        derived from the consolidated financial statements that have been
        audited by the Company's 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 the annual consolidated financial statements and
        notes of the Company. It is suggested that the accompanying condensed
        consolidated financial statements be read in conjunction with the
        audited consolidated financial statements and the notes thereto
        contained in the Company's Annual Report on Form 10-K for the fiscal
        year ended January 2, 1999, filed with the Securities and Exchange
        Commission.

        The preparation of the Company's consolidated financial statements in
        conformity with generally accepted accounting principles necessarily
        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 consolidated balance sheet dates and the
        reported amounts of revenues and expenses for the periods presented.

        Certain reclassifications have been made to the 1998 amounts to conform
        to the 1999 presentation.

2.      RECENTLY ISSUED ACCOUNTING STANDARD

        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 hedging accounting when certain conditions are met. Such
        Statement is effective for all fiscal quarters of fiscal years beginning
        after June 15, 2000. The Company will evaluate the new standard to
        determine any required new disclosures.


                                       6
<PAGE>   7
3.      INVENTORIES

        Inventories consist of the following:

<TABLE>
<CAPTION>
                                October 2, 1999      January 2, 1999
                                ---------------      ---------------
<S>                             <C>                  <C>
         Finished goods           $3,703,191           $2,712,543

         Work in process           2,146,032            1,456,784

         Raw materials             1,197,264            1,121,418
                                  ----------           ----------

         Total                    $7,046,487           $5,290,745
                                  ==========           ==========
</TABLE>


4.      EARNINGS PER SHARE

        The Company calculates basic earnings per share (EPS) and diluted EPS in
        accordance with Statement of Financial Accounting Standards No. 128,
        "Earnings per Share" (SFAS 128). Basic EPS is computed by dividing net
        income (loss) for the period by the weighted average number of common
        shares outstanding for that period. Diluted EPS takes into account the
        effect of dilutive instruments, such as stock options, 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 the three months and nine months
        ended October 2, 1999 and the three months and nine months ended October
        3, 1998 exclude any effect of such instruments because their inclusion
        would be antidilutive.

        The following is a summary of the calculation of the number of shares
        used in calculating basic and diluted EPS:

<TABLE>
<CAPTION>
                                                       Three Months Ended                  Nine Months Ended
                                                  ----------------------------        ----------------------------
                                                  October 2,        October 3,        October 2,        October 3,
                                                     1999              1998              1999              1998
                                                  ----------        ----------        ----------        ----------
<S>                                               <C>               <C>               <C>               <C>
        Shares used to compute basic EPS          20,455,018        20,355,375        20,439,394        20,320,976
        Add: effect of dilutive securities                 -                 -                 -                 -
                                                  ----------        ----------        ----------        ----------
        Shares used to compute diluted EPS        20,455,018        20,355,375        20,439,394        20,320,976
                                                  ==========        ==========        ==========        ==========
</TABLE>


                                       7
<PAGE>   8
5.      DISTRIBUTOR AGREEMENT

        During the first quarter of 1999, the Company 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 the Thoratec Vectra(TM) Vascular Access Graft
        product line, except in Japan. In exchange for these rights, Guidant has
        paid Thoratec a non-refundable payment of $1.5 million, and will pay up
        to an additional $2 million when the Vectra(TM) product line receives
        FDA approval for use in the U.S. Guidant also issued a four-year,
        unsecured line of credit in the amount of $10 million to Thoratec, which
        may be used, if needed, for a variety of business purposes. The Company
        will account for the $1.4 million (net of expenses) contract payment
        received in the first quarter of 1999 as revenue ratably over the
        five-year life of the contract. Other income in 1999 included $71,000
        and $214,000 of such payment amortization in the third quarter and nine
        months, respectively. Current liabilities of $285,000 and long-term
        liabilities of $925,000 are also reported as remaining balances as of
        October 2, 1999.


                                       8
<PAGE>   9
ITEM 2. MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS
        OF OPERATIONS

Liquidity and Capital Resources

At the end of the third quarter of 1999 the Company had working capital of
$11,187,000 compared with $11,251,000 at the end of 1998. The decrease in
working capital was due to a decrease in current assets, driven by an increase
in inventory offset by decreases in prepaid expenses, accounts receivable and
cash. Inventories increased in preparation for planned increases in sales
activity. Cash was used to support ongoing operations as well as planned
expenditures for the Company's new manufacturing facility. Accounts receivable
decreased because September 1999 sales were lower than December 1998 sales.
Prepaid expenses decreased due to amortization of insurance and property taxes.
Additionally, current liabilities increased slightly due to an increase in
deferred distributor revenue, partially offset by the payment of accrued bonuses
and commissions from the prior year. During the first quarter of 1999, the
Company entered into a five-year distribution agreement with Guidant Corporation
under which Guidant receives exclusive worldwide marketing and distribution
rights to the Thoratec Vectra(TM) Vascular Access Graft (VAG) product line,
except in Japan. In exchange for these rights, Guidant has paid Thoratec a
non-refundable payment of $1.5 million, and will pay up to an additional $2
million when the Vectra(TM) product line receives FDA approval for use in the
U.S. The Company received $1.4 million, net of expenses, in conjunction with
this distribution agreement in the first quarter of 1999. Since the payment will
be amortized into revenue over twenty quarters, $214,000 was recorded in other
income in the first nine months of 1999. $285,000 of current and $925,000 of
long-term deferred distributor revenue liabilities were also reported as
remaining balances at the end of the third quarter of 1999. Guidant also issued
a four-year, unsecured line of credit in the amount of $10 million to Thoratec,
which may be used, if needed, for a variety of business purposes.

The Company believes it has sufficient funds to increase its marketing efforts,
to conduct clinical trials on its new products, and to develop new sources of
revenue, including new products, for at least the next year. The Company expects
that its operating expenses will increase in future periods as the Company
expends increased amounts on product manufacturing, marketing and research and
development of new product lines. There can be no assurance that the Company
will achieve profitability or positive cash flow.

The Company does not expect that inflation will have a material impact on its
operations.

Results of Operations

Fiscal Quarters Ended October 2, 1999 and October 3, 1998

Product sales in the third quarter of 1999 were approximately $5,076,000
compared to $3,618,000 in the third quarter of 1998. The $1,458,000, or 40%,
increase is primarily due to increases in the number of domestic and
international centers using the VAD System as well as increases in the average
selling price of the VAD System for domestic and international customers.
Included in product sales is rental income in the third quarter of 1999 of
approximately $340,000 compared to $215,000 in the third quarter of 1998.
Interest and other income in the third quarter of 1999 were slightly higher when
compared to the third quarter of 1998. The increase was due to higher revenue
from the skeletal muscle project grant and $71,000 of revenue recognized in
other income as a result of the amortization of the $1.4 million Guidant payment
as described in the "Liquidity and Capital Resources" section above. These
increases were primarily offset by less interest income earned on lower cash
balances. Cost of sales increased $844,000


                                       9
<PAGE>   10
or 57%, in the third quarter of 1999. The increase is due to higher sales in the
third quarter 1999 compared to the third quarter 1998, higher fixed costs of the
new manufacturing facility, one-time costs associated with TLC-II(TM) Portable
VAD Driver component issues, adjustments from validation work on the graft
products, and other adjustments remaining from the Company's relocation of its
manufacturing operations in the second quarter 1999. Gross margin decreased from
59% in the third quarter of 1998 to 54% in the third quarter of 1999 due to
higher costs of goods sold as previously discussed, partially offset by
increases in the average selling price of the VAD System. Research and
development expenses for the third quarter of 1999 increased $245,000, or 20%,
compared to the third quarter of 1998. The increase in R&D expense relates to
efforts to resolve the TLC-II(TM) component issues, a transition from prototype
to pre-production on the implantable VAD project, and higher costs in the
Vectra(TM) trial. Selling, general and administrative expenses in the third
quarter of 1999 increased $680,000 or 41% compared to the third quarter of 1998
due to increased spending associated with strategic corporate planning and an
increase in the general level of business activity, including increased
personnel costs.

Nine Months Ended October 2, 1999 and October 3, 1998

Product sales in the first nine months of 1999 were approximately $15,343,000
compared to $11,330,000 in the first nine months of 1998. The $4,013,000 or 35%
increase is due to increases in the number of domestic and international centers
using the VAD System as well as increases in the average selling price of the
VAD System for domestic customers. Included in product sales is rental income in
the first nine months of 1999 of approximately $916,000 compared to $832,000 in
the first nine months of 1998. Interest and other income in the first nine
months of 1999 increased slightly to $529,000 compared to $524,000 in the first
nine months of 1998 due to lower interest income on overall lower cash balances
from operating uses and capital expenditures offset by increases from the
skeletal muscle project grant and $214,000 of revenue recognized in other income
as a result of the amortization of the $1.4 million Guidant payment as described
in the "Liquidity and Capital Resources" section above. Cost of sales increased
$1,875,000, or 42%, in the first nine months of 1999 compared to the first nine
months of 1998. The increase is due principally to higher sales in the first
nine months of 1999 compared to the first nine months of 1998 and also the
effect of some one-time costs associated with the TLC-II component issues,
adjustments from validation work on graft products and other adjustments
remaining from the Company's relocation of its manufacturing operations in the
second quarter of 1999. Gross margin decreased from 61% in the first nine months
of 1998 to 59% in the first nine months of 1999. The decrease is due to higher
costs of goods sold, partially offset by increased average selling price of the
VAD System. Research and development expenses for the first nine months of 1999
increased $190,000, or 5%, compared to the first nine months of 1998 due
principally to costs associated with the transition from prototype to
pre-production on the implantable VAD project, and higher costs in the
Vectra(TM) trial partially offset by a reduction in regulatory filing
preparation costs in Canada related to the Aria(TM) product. Selling, general
and administrative expenses in the first nine months of 1999 increased
$1,380,000 or 25% compared to the first nine months of 1998 due to overall
increases in the sales and marketing activities, including increased personnel
costs, and increased spending associated with strategic corporate planning,
general corporate overhead and operating expenses related to the Pleasanton
facility.

Other Matters

Year 2000 Readiness Disclosure

The Year 2000 issue involves computer programs and embedded microprocessors in
computer systems and other equipment that utilize two digits rather than four to
define the applicable year. These systems may be programmed to assume that all
two-digit dates are preceded by "19", causing "00" to be


                                       10
<PAGE>   11
interpreted as 1900 versus 2000. This could result in the possible failure of
those programs and devices to properly recognize date sensitive information when
the year changes to 2000. Systems that do not properly recognize date sensitive
information could generate erroneous data or a system failure. The Company's
objective is to ensure an uninterrupted transition into Year 2000 and has a plan
currently in place. The scope of the Year 2000 plan includes: (1) information
technology ("IT") such as software and hardware; (2) non-IT systems or embedded
technology such as microcontrollers contained in various manufacturing and lab
equipment, environmental and safety systems, facilities and utilities and
Company products with date sensitivity; and (3) readiness of key third parties,
including suppliers, customers and key financial institutions.

The Company has a formal Year 2000 compliance project that addresses the
Company's information technology systems. The Company has identified the
following phases of its Year 2000 project: 1) educate IT personnel and company
management about Year 2000 issue, 2) identify required resources to execute the
Year 2000 action plan, 3) create priority schedule for critical systems, 4)
estimate total cost of Year 2000 action plan, 5) determine and implement
corrections to non-compliant systems, 6) test and verify corrections, 7) place
corrected systems into service, and 8) monitor Year 2000 compliance with new
vendors, software and hardware. Phases 1 through 5 have been completed. Phases 6
and 7 are on schedule to be completed by the end of 1999. Phase 8 will continue
into the year 2000.

The Company has requested written confirmation from what it believes to be all
of its significant vendors as to their Year 2000 compliance status, and has
taken steps to determine the extent to which the Company's systems are
vulnerable to those third parties' failures to remedy their own Year 2000
issues. There can be no assurance that the systems of other companies with which
the Company does business will be timely converted or that any such failure to
upgrade or convert would not have an adverse effect on the Company's systems and
operations. However responses to date have indicated no significant problems.

Through the third quarter 1999, the Company has incurred less than $25,000 of
Year 2000 costs and expects to spend less than $10,000 during each of 1999 and
2000. All costs associated with Year 2000 compliance are being funded with cash
flow generated from operations and existing cash balances and are being expensed
as incurred.

The Company believes that the most reasonably likely worst-case scenario arising
from the Year 2000 issue is a temporary interruption in the Company's operations
resulting from non-compliant systems of third parties. Based on the status of
its Year 2000 compliance program, the Company currently believes that the Year
2000 issue will not pose significant operational problems for the Company's
internal computer systems. However, the company does not have, nor plan to have,
a formal contingency plan in the event its Year 2000 compliance program is
unsuccessful or not completed on a timely basis.

Forward-Looking Statements

The portions of this report that relate to future plans, events or performance
are forward-looking statements. Investors are cautioned that all such statements
involve risks and uncertainties, including risks related to the government
regulatory approval processes, delays in product development and new product
introductions, announcements by the Company's competitors, rapidly changing
technology, an intensely competitive market, market acceptance of new products,
relationships with foreign distributors, reimbursement policies and general
economic conditions. These factors, and others, are discussed more fully in the
Company's annual report on Form 10-K for the fiscal year ended January 2, 1999,
and the Company's 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.


                                       11
<PAGE>   12
The Company undertakes no obligation to publicly release the result of any
revisions to these forward-looking statements that may be made 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

The Company does not use derivative financial instruments in its operations or
investment portfolio. The Company does not have material exposure to market risk
associated with changes in interest rates as it has no long-term debt
obligations outstanding. The Company does not believe it has any other material
exposure to market risk associated with interest rates.

The Company sells to customers in foreign markets through our foreign
operations. These transactions are often denominated in currencies other than
the U.S. dollar. Our primary currency exposures are the British Pound and the
Euro. Foreign currency transaction gains and losses were not material to the
Company's results of operations for the quarter ended October 2, 1999. However,
the Company has experienced material fluctuations in intercompany foreign
currency translations as of the end of the first, second and third quarters of
1999 due to changes in the British Pound exchange rate. To date, the Company has
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.

                           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.


                                       12
<PAGE>   13
                                   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 5, 1999                      /s/ D. Keith Grossman
                             ---------------------------------------------------
                                 D. Keith Grossman, Chief Executive Officer

Date: November 5, 1999                       /s/ Cheryl D. Hess
                             ---------------------------------------------------
                                   Cheryl D. Hess, Chief Financial Officer


                                       13
<PAGE>   14
                                  EXHIBIT INDEX

<TABLE>
<CAPTION>
          Exhibit Number                                  Document
          --------------                                  --------
<S>                                                <C>
               27                                  Financial Data Schedule
</TABLE>


                                       14