<PAGE>   1
                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION


                             Washington, D.C. 20549

                                    FORM 10-Q


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

For the quarterly period ended March 31, 1997

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

For the Transition period from ________ to _______

                         Commission File Number: 0-28424

                            CARDIOGENESIS CORPORATION

             (Exact name of registrant as specified in its charter)


             Delaware                                      77-0352469
  -------------------------------                      -------------------
  (State or other jurisdiction of                       (I.R.S. employer
  incorporation or organization)                       identification No.)

                               540 OAKMEAD PARKWAY
                           SUNNYVALE, CALIFORNIA 94086
          (Address of principal executive offices, including zip code)

                                 (408) 328-8500
              (Registrant's telephone number, including area code)


Indicate by check mark whether the registrant (1) has filed all reports required
to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during
the preceding 12 months (or for such shorter period that the registrant was
required to file such reports), and (2) has been subject to such filing
requirements for the past 90 days.

                                Yes [ X ]    No [ ]

The number of shares of Common Stock outstanding as of April 17, 1997 was
  12,004,654.  




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                            CARDIOGENESIS CORPORATION

                                TABLE OF CONTENTS


<TABLE>
<CAPTION>
                                                                                              PAGE
<S>                <C>                                                                         <C>
PART I.            FINANCIAL INFORMATION

ITEM 1.            FINANCIAL STATEMENTS

                   Condensed Consolidated Balance Sheets as of March 31, 1997                   3
                            and December 31, 1996

                   Condensed Consolidated Statements of Operations for the three months         4
                            ended March 31, 1997 and 1996

                   Condensed Consolidated Statements of Cash Flows for the three months         5
                            ended March 31, 1997 and 1996

                   Notes to Condensed Consolidated Financial Statements                         6

ITEM 2.            MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION                  7
                    AND RESULTS OF OPERATIONS

ITEM 3.            QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK                  10

PART II.           OTHER INFORMATION


ITEM 6.            EXHIBITS AND REPORTS ON FORM 8-K                                            11


SIGNATURE                                                                                      12

INDEX TO EXHIBITS                                                                              13
</TABLE>




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<PAGE>   3


                            CARDIOGENESIS CORPORATION
                      Condensed Consolidated Balance Sheets
                                 (in thousands)
                                   (unaudited)


<TABLE>
<CAPTION>
                                                                                               March 31  December 31
                                                                                                 1997       1996
                                                                                               --------  -----------
<S>                                                                                             <C>        <C>    
                                                 ASSETS
Current assets:
    Cash and cash equivalents                                                                   $13,690    $ 2,080
    Available-for-sale securities                                                                39,054     53,626
    Accounts receivable, net                                                                      2,359      2,024
    Inventories                                                                                   1,175      1,108
    Other current assets                                                                          1,129      1,388
                                                                                                -------    -------
        Total current assets                                                                     57,407     60,226

    Property and equipment, net                                                                   1,504      1,546
    Available for sale securities, non-current                                                    2,502      2,502
    Other assets                                                                                     23         23
                                                                                                -------    -------
        Total assets                                                                            $61,436    $64,297
                                                                                                =======    =======

                                  TOTAL LIABILITIES AND STOCKHOLDERS' EQUITY
Current liabilities:
    Accounts payable and accrued expenses                                                       $ 3,412    $ 2,532
    Deferred revenue                                                                                 --       370
                                                                                                -------    -------
        Total liabilities                                                                         3,412     2,902

Stockholders' equity                                                                             58,024     61,395
                                                                                                -------    -------
        Total liabilities and stockholders' equity                                              $61,436    $64,297
                                                                                                =======    =======
</TABLE>




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




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<PAGE>   4


                            CARDIOGENESIS CORPORATION
                 Condensed Consolidated Statements of Operations
                      (in thousands, except per share data)
                                   (unaudited)


<TABLE>
<CAPTION>
                                           Three Months Ended March 31
                                           ---------------------------
                                                1997         1996
                                              --------      ------- 
<S>                                           <C>           <C>     
Sales                                         $  1,583      $   631 
Cost of sales                                    1,131          318 
                                              --------      ------- 
        Gross profit                               452          313 
                                              --------      ------- 
Operating expenses:                                                  
     Research and development                    3,254        1,574 
     General and administrative                    771          494 
     Sales and marketing                           801          303 
                                              --------      ------- 
        Operating expenses                       4,826        2,371 
                                              --------      ------- 
        Operating loss                          (4,374)      (2,058)
Interest income                                    779          180 
                                              ========      ======= 
        Net loss                              $ (3,595)     $(1,878)
                                              ========      ======= 
Net loss per share                            $  (0.30)     $ (0.43)
                                              ========      ======= 
Shares used in computing net                                        
     loss per share                             11,982        4,368 
                                              ========      ======= 
</TABLE>






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




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<PAGE>   5


                            CARDIOGENESIS CORPORATION
                 Condensed Consolidated Statements of Cash Flows
                                 (in thousands)
                                   (unaudited)

<TABLE>
<CAPTION>
                                                   Three Months Ended March 31
                                                   ---------------------------
                                                        1997         1996
                                                      --------      -------
<S>                                                   <C>           <C>     
Cash from operating activities:
     Net loss                                         $ (3,595)     $(1,878)
     Adjustments to reconcile net loss to
        net cash used in operating activities:
        Depreciation and amortization                      115           42
        Amortization of deferred compensation              137          396
        Disposal of property and equipment                  --            7
     Changes in assets and liabilities:
        Accounts receivable                               (335)         394
        Interest receivable                                324           --
        Inventories                                        (67)        (318)
        Prepaids and other                                 (65)         (80)
        Accounts payable and other                         823         (120)
        Accrued expenses                                   201          239
        Accrued compensation                              (100)         (14)
        Deferred revenue                                  (370)        (425)
        Short-term note payable                            (44)          --
                                                      --------      -------
            Net cash used in operating activities       (2,976)      (1,757)
                                                      --------      -------

Cash flows from investing activities:
     Purchase of available-for-sale securities          (5,378)      (1,927)
     Maturities of available-for-sale securities        19,950          415
     Acquisition of property and equipment                 (75)         (58)
     Other assets                                           --          (12)
                                                      --------      -------
            Net cash provided by (used in)
                investing activities                    14,497       (1,582)
                                                      --------       -------

Cash flows from financing activities:
     Proceeds from issuance of Preferred Stock,
        net of issuance costs                               --          240
     Proceeds from issuance of Common Stock,
        net of issuance costs                               89           64
                                                      --------      -------
        Net cash provided by financing activities           89          304

                                                      --------      -------
Net increase (decrease) in cash and cash equivalents    11,610       (3,035)
Cash and cash equivalents, beginning of period           2,080        4,150
                                                      ========      =======
Cash and cash equivalents, end of period              $ 13,690      $ 1,115
                                                      ========      =======
</TABLE>




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



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<PAGE>   6

                            CARDIOGENESIS CORPORATION

              NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS
                                   (UNAUDITED)

NOTE 1 - INTERIM CONSOLIDATED FINANCIAL STATEMENTS

         These interim consolidated financial statements are unaudited, but have
been prepared in accordance with generally accepted accounting principles for
interim information and with the instructions to Form 10-Q. In the opinion of
management, all adjustments (consisting of normal recurring accruals) considered
necessary for a fair presentation of financial position, results of operations
and cash flows at the dates and for the periods presented have been included.
The interim financial information herein is not necessarily indicative of
results for any future period. The interim consolidated financial statements
should be read in conjunction with the audited financial statements and the
notes thereto for the fiscal year ended December 31, 1996 included in the
Company's Form 10-K filed with the Securities and Exchange Commission.

NOTE 2 - INVENTORIES

         Inventories (in thousands) consisted of the following:

<TABLE>
<CAPTION>
                                              MARCH 31        DECEMBER 31
                                                1997              1996
                                              --------        -----------
                                                     (unaudited)
<S>                                            <C>              <C>   
                Raw materials                  $  193           $   20
                Finished goods                    992            1,088
                                               ------           ------
                                               $1,175           $1,108
                                               ======           ======
</TABLE>


NOTE 3 - LITIGATION

         On September 11, 1996, the Company filed an action for declaratory
relief against PLC Systems, Inc. of Canada and its wholly-owned American
subsidiary, PLC Medical Systems, Inc., (collectively, "PLC"), seeking a judgment
that PLC's United States patent No. 5,125,926 to a certain heart-synchronized
pulsed laser system is invalid and unenforceable. In the suit, filed in the
United States District Court for the Northern District of California, the
Company also requested the Court to enter judgment that the Company's
Transmyocardial Revascularization (TMR) systems do not infringe the PLC patent.
In October 1996, PLC responded to the complaint. In its response, PLC took the
position that its patent has been infringed by the Company, but made no further
claims.




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<PAGE>   7



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

This Report contains forward-looking statements within the meaning of Section
21E of the Securities Exchange Act of 1934, as amended. These forward-looking
statements involve a number of risks and uncertainties, including the factors
described throughout this Report, and in the Company's Form 10-K filed with the
Securities and Exchange Commission, particularly the section entitled
"Management's Discussion and Analysis of Financial Condition and Results of
Operations -- Risk Factors." The actual results the Company achieves may differ
materially from any forward-looking statements due to such risks and
uncertainties. The Company has identified by an asterisk (*) various sentences
within this Report which contain such forward-looking statements, and words such
as "believes", "anticipates", "expects", "intends" and similar expressions are
intended to identify forward-looking statements, but are not the exclusive means
of identifying such statements. The Company undertakes no obligation to revise
any forward-looking statements to reflect events or circumstances that may arise
after the date of this Report. Readers are urged to carefully review and
consider the various disclosures made by the Company in this Report and in the
Company's Form 10-K filed with the Securities and Exchange Commission that
attempt to advise interested parties of the risks and factors that may affect
the Company's business.

OVERVIEW

Since its inception, CardioGenesis has been primarily engaged in the design,
development, and marketing of its transmyocardial revascularization (TMR)
systems. The Company has a limited operating history and has experienced
significant operating losses since its inception. The Company incurred a net
loss of $3.6 million in the three months ended March 31, 1997. The development
and potential commercialization of the Company's products will require
significant research and development, regulatory, sales and marketing,
manufacturing and other expenditures. *Operating losses are expected to continue
at least through 1997 as the Company continues to perform research and
development, to fund clinical trials in support of regulatory and reimbursement
approvals, and to expand its marketing and sales activities in the U.S. and
internationally by supporting Boston Scientific Corporation (BSC). There can be
no assurance the Company's TMR systems will ever generate significant revenues
or the Company will achieve or sustain profitability.

The research, manufacture, sale and distribution of medical devices such as the
Company's TMR systems are subject to numerous regulations imposed by
governmental authorities, principally the Food and Drug Administration (FDA) and
corresponding state and foreign agencies. The regulatory process is lengthy,
expensive and uncertain. FDA approval of a Pre-market Approval (PMA) application
is required before any TMR system can be marketed in the United States. Securing
FDA approvals and clearances will require submission to the FDA of extensive
clinical data and technical information. Also, many foreign governments and the
European Union also have review processes for medical devices. In July 1996, the
Company received the CE Mark approval to market its ITMR System in the European
Community. The CE Mark is awarded to companies whose products meet the essential
requirements of the European Medical Device Directive (MDD) and provides the
regulatory approval necessary for commercialization. The Company will be subject
to continued supervision by regulators and will be required to report any
serious adverse incidents to the appropriate authorities. The Company also will
be required to comply with additional national requirements that are outside the
scope of the MDD. *The Company plans to continue to seek regulatory approvals to
allow for marketing and distribution of its products in international markets.

The Company commenced clinical trials of its intraoperative TMR (ITMR(TM))
System in October 1995 and began clinical trials of its percutaneous myocardial
revascularization (PMR(TM)) System in Europe in November 1996. In March 1997,
the Company reported it had filed an Investigational Device Exemption (IDE)
application with the FDA to conduct clinical investigations of its PMR System
in no-option patients. Clinical trials of the Company's thoracoscopic TMR
(TTMR(TM)) System have not commenced. In July 1996, the Company began a Phase
II clinical trial under an investigational device exemption (IDE) that allowed
a prospective, randomized, multi-center clinical trial of its ITMR System in
"no-option" patients with severe coronary artery disease (CAD). As of March 31,
1997, over 200 patients had been enrolled in this study. In August 1996, the
Company received an IDE from 





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<PAGE>   8

the FDA and has begun a clinical study of its ITMR System used as an adjunctive
therapy to coronary artery bypass graft (CABG) surgery in patients with severe
angina who are only partially treatable by CABG. *Substantial additional
clinical testing of the Company's TMR systems is required. The Company
continues to expect to file a PMA application for the ITMR System by the end of
1997.

The Company recorded sales of $1.6 million for the first three months of 1997
from sales of ITMR Systems and disposable ITMR probes to its international
distributor, BSC, in Europe and to clinical trial sites in the U.S. The Company
recognizes product revenues upon shipment of its products to customers and
fulfillment of acceptance terms, if any, and when no significant contractual
obligations remain outstanding. Deferred revenue consists of shipments that
have been made which are subject to limited rights of return or other
contingencies. *The Company anticipates its revenues from product sales over
the next several years will be primarily derived from international sales by
BSC. As a result, the revenue levels of the Company are and will be dependent
on the efforts of BSC in international markets *Any such international sales
will be subject to a number of risks, including foreign currency fluctuations,
economic or political instability, foreign tax laws, shipping delays, various
tariffs and trade regulations and restrictions and foreign medical regulations,
any of which could have a significant impact on the Company's revenues.

*Results of the Company's operations have varied and are expected to fluctuate
significantly from quarter to quarter depending on numerous factors, including:
(i) demand for the Company's products, new product introductions by the Company
or its competitors or transitions to new products; (ii) the timing of orders and
shipments; (iii) the degree of acceptance of TMR therapy by the medical
community; (iv) competition, including pricing pressures; (v) the timing of
regulatory and third-party reimbursement approvals; (vi) expansion of the
Company's manufacturing capacity and the Company's ability to manufacture its
products efficiently; (vii) the timing of research and development expenses,
including clinical trial-related expenditures, and (viii) seasonal factors
affecting the number of procedures performed. *Due to such fluctuations in
operating results, period-to-period comparisons of the Company's operating
results are not necessarily meaningful and should not be relied upon as
indicators of likely future performance.

RESULTS OF OPERATIONS

Three Months Ended March 31, 1997 and 1996

Sales. Sales of the Company's ITMR System for commercial use in Europe and for
use at clinical trial sites in both the U.S. and Europe increased approximately
$1.0 million to $1.6 million for the three months ended March 31, 1997 from
$631,000 for the three months ended March 31, 1996.

Cost of Sales. Cost of sales was approximately $1.1 million, or 71% of sales,
for the three months ended March 31, 1997 and $318,000, or 50% of sales, for the
same period in 1996. The increase in the percentage of cost of sales to sales is
primarily due to increases in operations and quality personnel and
implementation of systems in support of increasing production levels. 

Research and Development Expenses. Research and development expenses increased
$1.7 million to $3.3 million for the three months ended March 31, 1997 from $1.6
million for the same period in 1996. The increase in 1997 was primarily due to
the initiation of three additional clinical trials, two with the Company's ITMR
System and one with the PMR System. Also, the Company continued to invest in
mechanism research in the field of TMR. *The Company expects research and
development expenses to continue to increase throughout 1997 as the Company
continues to enroll patients in its ongoing clinical trials, initiates
additional clinical trials, and continues to invest in TMR mechanism research.

General and Administrative Expenses. General and administrative expenses
increased $277,000 to $771,000 for the three months ended March 31, 1997 from
$494,000 for the same period in 1996. The increase in 1997 was due to increased
finance and administration personnel costs to support the Company's growth and
comply with additional infrastructure requirements associated with being a
public company, increased legal fees associated with research and development
agreements and the exclusive international distribution agreement with 





                                      -8-
<PAGE>   9

BSC, legal fees related to the suit by the Company against PLC Medical Systems,
Inc. (PLC) seeking a judgment that a PLC patent is invalid and unenforceable,
increased property, general liability, and product liability insurance costs,
and public and investor relations program costs. *General and administrative
expenses should continue to increase in 1997.

Sales and Marketing Expenses. Sales and marketing expenses increased $498,000
to $801,000 for the three months ended March 31, 1997 from $303,000 for the
same period in 1996. The increase in 1997 was due to adding sales and marketing
personnel and the implementation of marketing and training programs. *Sales and
marketing expenses should continue to increase in 1997, but at a reduced rate
of growth, as the Company expands clinical studies, conducts physician
training, and supports the sales and marketing activities of BSC.

Interest Income. Interest income increased $599,000 to $779,000 for the three
months ended March 31, 1997 from $180,000 for the same period in 1996. The
increase in 1997 is due to the investment of the proceeds from the Company's
initial public offering of Common Stock in May 1996 of approximately $54.5
million, net of issuance costs.

Deferred Compensation Expense. The Company recorded deferred compensation
expense of approximately $2.3 million with respect to options to purchase Common
Stock granted and Preferred Stock issued during 1996 and 1995. Deferred
compensation expense is being amortized over the vesting period of the options,
which is generally four years. The Company recognized compensation expense of
$137,000 and $396,000 for the three months ended March 31, 1997 and 1996,
respectively.

LIQUIDITY AND CAPITAL RESOURCES

The Company has funded its operations since inception primarily through the
private sale of capital stock and interest income on proceeds from private
financings as well as from its initial public offering in May 1996. Through
March 31, 1997, the Company had raised approximately $77.2 million from the sale
of stock, net of issuance costs.

Net cash used in the Company's operations was $3.0 million and $1.8 million for
the three months ended March 31, 1997 and 1996, respectively. The increases in
net cash used in the Company's operations were primarily a result of increased
levels of research and development, general and administrative, and sales and
marketing activities. The Company's acquisition of property and equipment was
$74,000 and $58,000 for the three months ended March 31, 1997 and 1996,
respectively. *The Company expects similar levels of capital expenditures
during the rest of 1997.

At March 31, 1997, the Company had cash, cash equivalents, and
available-for-sale securities, of $55.2 million. *The Company plans to finance
its operations and capital needs principally from the cash, cash equivalents,
and available-for-sale securities, and, to the extent available, from bank and
lease financing and believes these sources of cash will be sufficient to fund
its operations at least through 1998. *However, the Company's future liquidity
and capital requirements will depend upon numerous factors, including the level
of sales generated by BSC in major and emerging international markets; market
acceptance of, and demand for the Company's products; the Company's clinical
research and product development programs; the receipt of, and the time required
to obtain, regulatory clearances and approvals; the resources the Company
devotes to the development, manufacture and marketing of its products; the
resources required to hire and develop a direct sales force in the United
States, and to expand manufacturing capacity; facilities requirements; and other
factors. *Although the Company believes the current levels of cash, cash
equivalents, and available-for-sale securities, together with cash generated
from operations, will provide adequate funding for its operations and capital
requirements through at least 1998, the Company may be required to raise
additional funds through public or private debt or equity financings,
collaborative relationships, bank facilities or other arrangements. *There can
be no assurance the Company will not require additional funding sooner or that
such additional funding, if needed, will be available on terms attractive to the
Company, or at all. *Any additional equity financing may be dilutive to
stockholders, and debt financing, if available, may involve restrictive
covenants.





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ITEM 3.  QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

         Not applicable.



                                        
                                        
                                       -10-
<PAGE>   11

PART II.   OTHER INFORMATION


ITEM 6.    EXHIBITS AND REPORTS ON FORM 8-K

         (a)   Exhibits

   Number      Description
   ------      -----------

   11.01       Statement Regarding Computation of Net Loss Per Share

   27.01       Financial Data Schedule


         (b)   Reports on Form 8-K

                  none








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                                    SIGNATURE

         Pursuant to the requirements of the Securities Exchange Act of 1934,
the Registrant has duly caused this report to be signed on its behalf by the
undersigned thereunto duly authorized.


                              CARDIOGENESIS CORPORATION
                              (Registrant)




Date: May 14, 1997            By:  /s/ Richard P. Powers
                                  ---------------------------------------------
                                  Richard P. Powers
                                  Chief Financial Officer, Vice President of
                                  Finance and Administration, and Secretary
                                  (Duly Authorized Officer, Principal Financial
                                  Officer, and Principal Accounting Officer)









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<PAGE>   13



                                INDEX TO EXHIBITS


   EXHIBIT
   -------

    11.01      Statement Regarding Computation of Net Loss Per Share

    27.01      Financial Data Schedules









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