<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 April 3, 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 Registrant as Specified in Its Charter)


          California                                     94-2340464
-------------------------------                   ------------------------------
(State or Other Jurisdiction of                       (I.R.S. Employer
Incorporation or                                     Identification No.)
Organization)

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 May 12, 1999 registrant had 20,437,486 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>
                                                                  April 3,             January 2,
                                                                    1999                  1999
                                                                ------------          ------------
<S>                                                             <C>                   <C>         
ASSETS

Current Assets:

Cash and cash equivalents                                       $  2,369,166          $  2,712,686

Short-term investments available-for-sale                          2,079,965             2,032,107

Receivables, net                                                   4,504,801             4,141,854

Inventories (Note 3)                                               5,348,090             5,290,745

Prepaid expenses and other                                           355,666               404,737
                                                                ------------          ------------

Total current assets                                              14,657,688            14,582,129

Equipment and improvements, at cost                               12,672,246            12,460,755

Accumulated depreciation and amortization                         (3,029,996)           (2,835,365)
                                                                ------------          ------------

Equipment and improvements - net                                   9,642,250             9,625,390

Other assets                                                       1,009,307             1,000,898
                                                                ------------          ------------

TOTAL ASSETS                                                    $ 25,309,245          $ 25,208,417
                                                                ============          ============


LIABILITIES AND SHAREHOLDERS' EQUITY

Current Liabilities:

Accounts payable                                                $  1,217,713          $  1,307,768

Accrued compensation                                                 853,003             1,613,334

Product sales advances                                               144,952               121,373

Deferred distributor revenue (Note 5)                                284,760

Other                                                                357,573               288,585
                                                                ------------          ------------

Total current liabilities                                          2,858,001             3,331,060

Long-term deferred distributor revenue (Note 5)                    1,067,871
                                                                ------------          ------------

Total liabilities                                                  3,925,872             3,331,060

Commitments

Shareholders' Equity:
Common shares, 100,000,000 authorized; issued and
  outstanding 20,432,812 in 1999 and 20,422,952 in 1998           72,845,977            72,810,450

Additional capital                                                 2,482,229             2,482,229

Accumulated deficit                                              (53,737,718)          (53,402,106)

Accumulated other comprehensive loss:

Unrealized gain (loss) on investments - net                             (912)                    8

Cumulative translation adjustments                                  (206,203)              (13,224)
                                                                ------------          ------------

Total accumulated other comprehensive loss                          (207,115)              (13,216)
                                                                ------------          ------------

Total shareholders' equity                                        21,383,373            21,877,357
                                                                ------------          ------------

TOTAL LIABILITIES AND SHAREHOLDERS' EQUITY                      $ 25,309,245          $ 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
                                                 -----------------------------------
                                                 April 3, 1999         April 4, 1998
                                                 -------------         -------------
<S>                                               <C>                   <C>         

Revenue:
  Product sales - net                             $  5,375,473          $  3,503,064
  Interest and other income  (Note 5)                  170,276               199,845
                                                  ------------          ------------


  Total revenue                                      5,545,749             3,702,909
                                                  ------------          ------------


Costs and expenses:
  Costs of products sold                             2,347,598             1,356,592
  Research and development                           1,153,225             1,220,060
  Selling, general and administrative                2,380,538             1,800,467
                                                  ------------          ------------

  Total costs and expenses                           5,881,361             4,377,119
                                                  ------------          ------------

Net loss                                              (335,612)             (674,210)
                                                  ============          ============

Basic and diluted loss per share (Note 4)         $      (0.02)         $      (0.03)
                                                  ============          ============


Shares used to compute loss per share               20,426,011            20,285,232

</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
                                                 --------------------------------
                                                 April 3, 1999      April 4, 1998
                                                 -------------      -------------
<S>                                              <C>                <C>       
Net loss                                           $(335,612)         $(674,210)
                                                   ---------          ---------

Other comprehensive income (loss):
  Unrealized gain (loss) on investments                 (920)             6,502
  Foreign currency translation adjustments          (192,979)            23,740
                                                   ---------          ---------
Other comprehensive income (loss)                   (193,899)            30,242
                                                   ---------          ---------

Comprehensive loss                                 $(529,511)         $(643,968)
                                                   =========          =========

</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>
                                                                       Three Months Ended
                                                               ----------------------------------
                                                               April 3, 1999        April 4, 1998
                                                               -------------        -------------
<S>                                                            <C>                  <C>         
Cash flows from operating activities:
     Net loss                                                   $  (335,612)         $  (674,210)
     Adjustments to reconcile net loss to net cash used in
     operating activities:
       Depreciation and amortization                                201,418              159,292
       Amortization of deferred distributor revenue (Note 5)        (71,192)

       Changes in assets and liabilities:
             Receivables                                           (406,359)            (859,263)
             Prepaid expenses and other                              47,091               (4,477)
             Inventories                                            (92,491)            (686,282)
             Other assets                                            (8,586)             (16,369)
             Accounts payable and other liabilities                (807,033)            (311,643)
             Deferred distributor revenue                         1,423,823
                                                                -----------          -----------
 Net cash used in operating activities                              (48,941)          (2,392,952)
                                                                -----------          -----------

Cash flows from investing activities:
    Purchases of short-term investments                          (2,930,041)          (5,063,978)
      available-for-sale
    Maturities of short-term investments                          2,615,000            4,925,000
      available-for-sale
    Sales of short-term investments available-for-sale              266,263               72,881
    Capital expenditures                                           (265,614)          (1,811,876)
                                                                -----------          -----------
         Net cash used in investing activities                     (314,392)          (1,877,973)
                                                                -----------          -----------

Cash flows from financing activities:
    Common stock issued upon exercise of options                     35,527               19,332
                                                                -----------          -----------
         Net cash provided by financing activities                   35,527               19,332
                                                                -----------          -----------

Effect of exchange rate changes on cash                             (15,714)               1,420
                                                                -----------          -----------

Net decrease in cash and cash equivalents                          (343,520)          (4,250,173)

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

Cash and cash equivalents at end of period                      $ 2,369,166          $ 5,219,138
                                                                ===========          ===========

Noncash Financing Transaction:
      Construction  costs and capital assets in accounts 
        payable                                                 $    43,777          $ 2,452,549

</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 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
        April 3, 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 condensed 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.

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


2.      RECENTLY ISSUED ACCOUNTING STANDARD

        In June 1998, the Financial Accounting Standards Board (FASB) issued
        Statement of Financial Accounting Standards (SFAS) No. 133,
        "Accounting for Derivative Instruments and Hedging Activities," which is
        effective for fiscal years beginning after June 15, 1999. The Company
        will evaluate the new standard to determine any required new
        disclosures.


3.      INVENTORIES

        Inventories consist of the following:

<TABLE>
<CAPTION>
                       April 3, 1999     January 2, 1999
                       -------------     ---------------
<S>                    <C>               <C>       
Finished goods          $2,933,930         $2,712,543

Work in process          1,051,975          1,456,784

Raw materials            1,362,185          1,121,418
                        ----------         ----------

Total                   $5,348,090         $5,290,745
                        ==========         ==========
</TABLE>




                                       6
<PAGE>   7





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 1999 and 1998 are the same as
        basic EPS due to the Company reporting net losses in these periods.

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

<TABLE>
<CAPTION>
                                                     FISCAL YEAR
                                            -----------------------------
                                               1999               1998
                                            ----------         ----------
<S>                                         <C>                <C>       
Shares used to compute basic EPS            20,426,011         20,285,232
Add:  effect of dilutive securities                 --                 --
                                            ----------         ----------
Shares used to compute diluted EPS          20,426,011         20,285,232
                                            ==========         ==========
</TABLE>


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 the first quarter of
        1999 included $71,000 of such payment amortization. Current liabilities
        of $285,000 and long-term liabilities of $1,068,000 were also recorded
        since the payment will be amortized over twenty quarters.



                                       7
<PAGE>   8


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

Liquidity and Capital Resources

At the end of the first quarter of 1999 the Company had working capital of
$11,800,000 compared with $11,251,000 at the end of 1998. The increase in
working capital was due to (a) an increase in current assets, driven by
increases in receivables and inventory partially offset by a decrease in cash,
and (b) a decrease in current liabilities, primarily driven by a decrease in
accrued compensation partially offset by an increase in short-term deferred
distributor revenue. 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 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, $71,000 was recorded in other income and $285,000 of current
and $1,068,000 of long-term deferred distributor revenue liabilities were also
recorded in the first 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. Cash was used during the
quarter to support ongoing operations as well as to purchase new equipment for
the Company's Pleasanton facility and to fund expanded sales and marketing
programs directed to open heart surgery centers for the VAD in the U.S. and the
TLC II(TM) Portable VAD Driver marketing effort in Europe. Receivables increased
principally due to higher sales in March compared to December. Equipment
increased due to purchases of office furniture for the Pleasanton facility and
lab equipment for product development.

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. The Company expects to break even in the
current year. However, 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 April 3, 1999 and April 4, 1998

Product sales in the first quarter of 1999 were approximately $5,375,000
compared to $3,503,000 in the first quarter of 1998. The $1,872,000, or 53%,
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 domestically. Included in product sales is rental income in the first
quarter of 1999 of approximately $325,000 compared to $275,000 in the first
quarter of 1998. The $50,000, or 18%, increase is principally due to new and
existing centers renting drivers rather than purchasing the equipment. Interest
and other income in the first quarter of 1999 decreased $30,000 or 15%. The
decrease is due to overall lower cash balances partially offset by revenue
received on 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.
Cost of sales increased $991,000, or 73%, in the first quarter of 1999 primarily
as a result of higher sales. Gross margin as a percentage of sales decreased in
the first quarter of 1999 compared to the first quarter of 1998 due to the
impact of non-recurring expenses associated with the transfer of manufacturing
operations to the Company's new Pleasanton facility in March 1999, and start-up


                                       8
<PAGE>   9



expenses associated with scaling up the TLC II(TM) for production. Research and
development expenses for the first quarter of 1999 decreased $67,000, or 5%,
compared to the first quarter of 1998. The decease in research and development
expenses is primarily a result of the completion of the TLC II(TM) project.
Research and development expenses are expected to increase in future quarters
due to higher clinical trial costs associated with the TLC II(TM) , Vectra(TM)
and Aria(TM) projects. Selling, general and administrative expenses in the
first quarter of 1999 increased $580,000, or 32%, compared to the first quarter
of 1998. Selling general and administrative expenses increased primarily due to
growth of sales and marketing personnel and related costs and increased
operating expenses related to the Pleasanton facility.
        
OTHER MATTERS

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 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; (3) and 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 noncompliant 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 4 have been completed. Phase 5
is currently in process and is scheduled for completion by July 1999. 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 first quarter 1999, the Company has incurred less than $25,000 of Year
2000 cost 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.



                                       9
<PAGE>   10


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 April 3, 1999. However,
the Company has experienced a material fluctuation in intercompany foreign
currency translation as of the end of the first quarter of 1999 due to a decline
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.


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 announcements by the Company's
competitors, risks related to the government regulatory approval processes,
delays in product development and new product introductions, 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. 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.



                                       10
<PAGE>   11



                           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.






                                       11
<PAGE>   12



                                   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:  May 12, 1999                          /s/ D. Keith Grossman
       -------------                  ------------------------------------------
                                      D. Keith Grossman, Chief Executive Officer


Date:  May 12, 1999                         /s/ Cheryl D. Hess
       -------------                  ------------------------------------------
                                      Cheryl D. Hess, Chief Financial Officer



                                       12
<PAGE>   13



                                  EXHIBIT INDEX



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

</TABLE>



                                       13