<PAGE>
 
                                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 June 30, 1998.

[_]    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
                                    0-20819
                                        

                                THERMATRIX INC.
             (Exact name of registrant as specified in its charter)

<TABLE>
<S>                                               <C>
              DELAWARE                                 94-2958515
        (State or other jurisdiction of               (IRS Employer
        incorporation or organization)             Identification Number)
</TABLE>

                           101 METRO DRIVE, SUITE 248
                          SAN JOSE, CALIFORNIA  95110
                    (Address of principal executive offices)

                                 (408) 453-0490
              (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 at least the past 90 days:

                             Yes     X         No ___________
                                ---------                    


        Indicate the number of shares outstanding of each of the issuer's
        classes of common stock, as of the latest practicable date:


           Class                  Outstanding at June 30, 1998
           -----                  ----------------------------   
Common stock, $.001 par value                7,869,330

<PAGE>
 
                                THERMATRIX INC.
                                        
This report contains forward-looking statements within the meaning of Section
27A of the Securities Act of 1933 and Section 21E of the Securities Exchange
Act of 1934. The Company's actual results could differ materially from those
anticipated in these forward-looking statements as a result of certain
factors, including those set forth under "Certain Business Considerations" in
"Management's Discussion and Analysis of Financial Condition and Results of
Operations" and elsewhere in, or incorporated by reference into, this report.


                              TABLE OF CONTENTS

 
PART I.                     FINANCIAL INFORMATION                     PAGE
                                                                      ----
 
Item 1.    Financial Statements.....................................    3
 
           Condensed Consolidated Balance Sheets....................    3
 
           Condensed Consolidated Statements of Operations..........    4
 
           Condensed Consolidated Statements of Cash Flows..........    5
 
           Notes to Condensed Consolidated Financial Statements.....    6
 
Item 2.    Management's Discussion and Analysis of Financial Condition
           and Results of Operations................................    8
 
PART II.   OTHER INFORMATION
 
Item 1.    Legal Proceedings........................................   14
 
Item 2.    Changes in Securities...................................    14
 
Item 3.    Defaults Upon Senior Securities.........................    14
 
Item 4.    Submission of Matters to a Vote of Security Holders.....    14
 
Item 5.    Other Information.......................................    14
 
Item 6.    Exhibits and Reports on Form 8-K........................    15
 
           SIGNATURE...............................................    16

                                       2
<PAGE>
 

                                THERMATRIX INC.
                     CONDENSED CONSOLIDATED BALANCE SHEETS
                     (In thousands, except share amounts)


<TABLE> 
<CAPTION> 
 
                                                                        JUNE 30,           DECEMBER 31,
                                                                         1998                  1997
                                                                  ------------------    ----------------
                                                                     (Unaudited)
<S>                                                             <C>                     <C> 
ASSETS
           CURRENT ASSETS
           Cash & cash equivalents                                          $  4,459            $  3,990
           Short-term investments                                              1,625               3,587
           Accounts receivable, net                                            4,291               3,520
           Costs of uncompleted contracts, net                                   355                 547
           Prepaid expenses and other current assets                             223                 250
                                                                  ------------------    ----------------
                Total current assets                                          10,953              11,894
 
           PROPERTY AND EQUIPMENT
           Machinery and equipment                                               798                 857
           Demonstration equipment                                               535                 506
           Furniture and fixtures                                                417                 322
                                                                  ------------------    ----------------
                                                                               1,750               1,685
           Less -  Accumulated depreciation and amortization                  (1,043)               (749)
                                                                  ------------------    ----------------
                   Net property and equipment                                    707                 936
                                                                  ------------------    ----------------
 
           PATENTS AND OTHER ASSETS, net                                       1,234               1,157
                                                                  ------------------    ----------------
 
                                                                            $ 12,894            $ 13,987
                                                                  ==================    ================
 
LIABILITIES AND STOCKHOLDERS' EQUITY
           CURRENT LIABILITIES
           Accounts payable                                                 $  2,416            $  1,055
           Accrued liabilities                                                   754                 802
           Billings on uncompleted contracts in excess of costs                  435                 181
                                                                  ------------------    ----------------
                   Total current liabilities                                   3,605               2,038
 
           STOCKHOLDERS' EQUITY:
                   Common stock, $0.001 par value                                  8                   8
                   Additional paid-in capital                                 48,749              48,644
                   Accumulated other comprehensive income                         13                   -
                   Accumulated deficit                                       (39,481)            (36,703)
                                                                  ------------------    ----------------
                           Total stockholders' equity                          9,289              11,949
                                                                  ------------------    ----------------
 
                                                                            $ 12,894            $ 13,987
                                                                  ==================    ================
</TABLE>

           See notes to condensed consolidated financial statements.

                                       3
<PAGE>
 


                                THERMATRIX INC.
                CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS
                     (In thousands, except per share data)
                                  (Unaudited)

<TABLE> 
<CAPTION> 

                                                        Three Months                            Six Months
                                                       Ended June 30,                          Ended June 30,
                                                --------------------------              -------------------------
                                                    1998           1997                      1998           1997
                                                -----------    -----------              -----------   -----------
<S>                                           <C>             <C>                     <C>             <C> 
REVENUES                                            $ 2,796        $ 2,250                 $ 5,678         $ 3,334
COST OF REVENUES                                      2,620          2,483                   5,147           3,889
                                                -----------    -----------              -----------   -----------
        Gross Margin                                    176           (233)                    531            (555)
                                                -----------    -----------              -----------   -----------

OPERATING EXPENSES:
    Research and development                            407            437                     662             620
    Selling, general and administrative               1,436          1,788                   2,866           3,432
                                                -----------    -----------              -----------   -----------
        Total operating expenses                      1,843          2,225                   3,528           4,052
                                                -----------    -----------              -----------   -----------
        Loss from operations                         (1,667)        (2,458)                 (2,997)         (4,607)
                                                -----------    -----------              -----------   -----------

OTHER INCOME:
    Interest income (net)                               105            183                     210             394
    Other income                                         42              1                      42               3
                                                -----------    -----------             -----------     -----------
        Total other income                              147            184                     252             397
                                                -----------    -----------             -----------     -----------
        Net loss before income taxes                 (1,520)        (2,274)                 (2,745)         (4,210)

PROVISION FOR INCOME TAXES                              (17)           (17)                    (33)            (33)
                                                -----------    -----------             -----------     -----------
        Net loss                                    $(1,537)       $(2,291)                $(2,778)        $(4,243)
                                                ===========    ===========             ===========     ===========

BASIC NET LOSS PER SHARE                            $ (0.20)       $ (0.30)                $ (0.36)        $ (0.57)
                                                ===========    ===========             ===========     ===========

BASIC WEIGHTED AVERAGE
COMMON SHARES                                         7,671          7,535                   7,653           7,503
                                                ===========    ===========             ===========     ===========
</TABLE> 

           See notes to condensed consolidated financial statements.

                                       4
<PAGE>
 


                                THERMATRIX INC.
                CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS
                                (In thousands)

<TABLE>
<CAPTION>



                                                                              SIX MONTHS ENDED
                                                                    ------------------------------------
                                                                         JUNE 30,            JUNE 30,
                                                                           1998                1997
                                                                    ----------------    ----------------
                                                                                 (Unaudited)
<S>    <C>                                                            <C>                 <C>

CASH FLOWS FROM OPERATING ACTIVITIES
       Net loss                                                              $(2,778)            $(4,243)
       Adjustments to reconcile net loss to net cash used in
       operating activities -
           Depreciation and amortization                                         379                 189
           Provision for doubtful accounts                                       129                  65
       Changes in assets and liabilities -
           Accounts receivable                                                  (900)                812
           Costs of uncompleted contracts                                        197                (188)
           Prepaid expenses and other                                             28                 (18)
           Accounts payable                                                    1,360                  42
           Accrued liabilities                                                   (49)               (176)
           Billings on uncompleted contracts in excess of costs                  253                  (8)
                                                                    ----------------    ----------------
       Net cash used in operating activities                                  (1,381)             (3,525)
                                                                    ----------------    ----------------
 
CASH FLOWS FROM INVESTING ACTIVITIES
       Sale of short-term investments                                          1,962               2,914
       Purchases of property and equipment                                       (65)               (245)
       Increase in patents and other assets                                     (162)               (176)
                                                                    ----------------    ----------------
       Net cash provided by investing activities                               1,735               2,493
                                                                    ----------------    ----------------
 
CASH FLOWS FROM FINANCING ACTIVITIES
       Net proceeds from sale of common stock                                    105                 101
                                                                    ----------------    ----------------
 
INCREASE (DECREASE) IN CASH & CASH EQUIVALENTS                                   459                (931)
 
CUMULATIVE EFFECT OF FOREIGN EXCHANGE RATES ON CASH                               10                   -

CASH & CASH EQUIVALENTS BEGINNING OF PERIOD                                    3,990               4,781
                                                                    ----------------    ----------------
 
CASH & CASH EQUIVALENTS END OF PERIOD                                        $ 4,459             $ 3,850
                                                                    ================    ================
 
SUPPLEMENTAL CASH FLOW INFORMATION
       Cash paid for interest                                                     13                   3
       Cash paid for income taxes                                                 78                  81
 
                                     See notes to condensed consolidated financial statements.
</TABLE>
                                        

                                       5
<PAGE>
 
                                THERMATRIX INC.
             NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS
                                 June 30, 1998
                                  (Unaudited)


1.   BASIS OF PRESENTATION

The accompanying condensed consolidated financial statements include the
accounts of the Company and its wholly owned subsidiary. The condensed
consolidated financial statements included herein have been prepared by the
Company, without audit, pursuant to the rules and regulations of the Securities
and Exchange Commission. Certain information and footnote disclosures normally
included in financial statements prepared in accordance with generally accepted
accounting principles have been condensed or omitted pursuant to such rules and
regulations. These condensed consolidated financial statements should be read in
conjunction with the consolidated financial statements and the notes thereto
included in the Company's Annual Report on Form 10-K for the year ended December
31, 1997.

The unaudited condensed consolidated financial statements included herein
reflect all adjustments (which include only normal, recurring adjustments) which
are, in the opinion of management, necessary to state fairly the results for the
three months and six months ended June 30, 1998 and 1997. The preparation of
financial statements in conformity with generally accepted accounting principles
requires management to make estimates and assumptions that affect the reported
amounts of assets and liabilities, the disclosure of contingent assets and
liabilities at the date of the financial statements and the reported amounts of
revenues and expenses during the reporting period. Actual results could differ
from those estimates. The results for the six months ended June 30, 1998 are not
necessarily indicative of the results expected for the full fiscal year.


2.   BASIC NET LOSS PER SHARE

Basic net loss per share is computed using the weighted average number of shares
of common stock outstanding. No diluted loss per share information has been
presented in the accompanying statements of operations since potential common
shares from conversion of stock options and warrants are antidilutive.


3.   SHORT-TERM INVESTMENTS

In accordance with the Statement of Financial Accounting Standards No. 115,
"Accounting for Certain Investments in Debt and Equity Securities," the Company
has classified all marketable debt securities as held-to-maturity and has
accounted for these investments at amortized cost. Short-term investments are
marketable securities with original maturities greater than three months and
less than one year. As of June 30, 1998, short-term investments consist
principally of certificates of deposit and commercial paper.


4.   COMPREHENSIVE INCOME

In June 1997, the Financial Accounting Standards Board issued SFAS No. 130 (SFAS
130), "Reporting Comprehensive Income," which establishes standards for
reporting and display of comprehensive income and its components (revenue,
expenses, gains and losses) in a full set of general-purpose financial

                                       6
<PAGE>
 
statements. The following table reconciles comprehensive income under the
provisions of SFAS 130 for the three months and six months ended June 30, 1998
and 1997.

<TABLE>
<CAPTION>
 
                                             For the Three Months Ended June 30
                                                    1998               1997
                                            ------------------------------------
<S>                                     <C>                  <C>
 
Net Loss                                           $(1,537)         $(2,291)
Other Comprehensive Loss, net of tax
     Unrealized Currency Loss                       (    7)         $     -
                                                   -------   --------------
Comprehensive Loss                                 $(1,544)         $(2,291)
                                                   =======          =======
 
 
                                               For the Six Months Ended June 30
                                                    1998               1997
                                            ------------------------------------
 
Net Loss                                           $(2,778)         $(4,243)
Other Comprehensive Loss, net of tax
     Unrealized Currency Gain                      $    13          $     -
                                                   -------   --------------
Comprehensive Loss                                 $(2,765)         $(4,243)
                                                   =======          =======
 
</TABLE>

5.   ACCOUNTING FOR DERIVATIVE INSTRUMENTS AND HEDGING ACTIVITIES

In June 1998, the Financial Accounting Standards Board issued SFAS No. 133,
Accounting for Derivative Instruments and Hedging Activities. The Statement
establishes accounting and reporting standards requiring that every derivative
instrument (including certain derivative instruments embedded in other
contracts) be recorded in the balance sheets as either an asset or liability
measured at its fair value. The Statement requires that changes in the
derivative's fair value be recognized currently in earnings unless specific
hedge accounting criteria are met. Statement 133 is effective for fiscal years
beginning after June 15, 1999. We have not yet quantified the impacts of
adopting Statement 133 on our financial statements and have not determined the
timing of or method of our adoption of Statement 133. However, the Statement
could increase volatility in earnings and other comprehensive income.

                                       7
<PAGE>
 
                                THERMATRIX INC.
          MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION
                           AND RESULTS OF OPERATIONS

The following discussion contains forward-looking information that involves
known and unknown risks and uncertainties which may cause the Company's actual
results in future periods to differ materially from those indicated herein as a
result of certain factors, including those set forth under "Certain Business
Considerations."

The following discussion should be read in conjunction with the unaudited
condensed consolidated financial statements and the notes thereto included in
Item 1 of this Quarterly Report and the audited consolidated financial
statements and notes thereto and Management's Discussion and Analysis of
Financial Condition and Results of Operations for the year ended December 31,
1997, contained in the Company's Annual Report on Form 10-K.

GENERAL
-------

Thermatrix Inc. is a global industrial technology company engaged in the
development, manufacture and sale of industrial process equipment for the
destruction of volatile organic compounds and hazardous air pollutants
(collectively "VOCs"). The core component of the Company's technology is its
proprietary flameless thermal oxidizer ("FTO"). The Company's products also
include PADRE(R), a proprietary technology used to capture and recover very low
concentration VOCs from low-to-medium flow vapor streams. In addition to its
primary focus on the industrial VOC emissions control market, the Company is
currently focusing its development activities on the application of its FTO
technology to treat emissions from diesel engines, both mobile and stationary.

The Company derives its revenues primarily from contracts to design, develop,
manufacture and install systems for the treatment of VOCs. The Company uses the
percentage-of-completion method of accounting to recognize contract revenues.
Losses on contracts are charged to cost of revenues as soon as such losses
become known.

The Company experienced a shift in market demand for its products during the
last eighteen months. In 1997, the United States VOC market declined,
reflecting, the Company believes, low capital expenditures in new process
facilities. However, the Company experienced an increase in demand for its
products overseas, primarily due to the continued globalization of the chemical
and pharmaceutical industries, increased adoption of ISO 14000 standards, and
capital expenditures by overseas companies. The Company responded to this shift
by reducing its United States sales and operating staff and increasing its
presence overseas. In 1998, the Company experienced positive momentum in its
global VOC business, particularly in Europe. The geographic split of the orders
received in 1998 is approximately 70% in Europe and 30% in the United States and
includes orders from the pharmaceutical, specialty chemical, refining and
remediation industries. The Company's revenues for the six months ended June 30,
1998 have increased by 70% over the same period in the prior year.

In addition to its primary focus on the industrial VOC emissions control market,
the Company is currently evaluating the feasibility of applying the Company's
technology to treat emissions from diesel engines. During the second quarter of
fiscal 1998, the Company announced the successful conclusion of an eighteen-
month testing and technology evaluation program and the completion of a joint
development project with Lucas Diesel Systems, a division of LucasVarity plc.
The testing and evaluation program provided for the development and testing of a
prototype system utilizing the Company's patented FTO technology for the
treatment of diesel engine emissions from mobile sources.

                                       8
<PAGE>
 
In the course of conducting this test program, the Company developed a new
configuration that would allow the technology to be downsized to enhance its
suitability for mobile applications while confirming the ability to inject
diesel fuel into the matrix core to maintain operating temperature. The results
of the testing show a level of control equal to or superior to any other
technology commercially available and significantly better than the U.S.
Environmental Protection Agency's proposed regulations for mobile sources
including trucks, off-road vehicles, locomotives and marine vessels.

Expenses incurred by the Company in connection with these development programs,
primarily labor and equipment operation costs, are generally recorded as
research and development expenses. The Company may also provide an evaluation
system as part of a joint development program, and if it does, the capital cost
of the evaluation system is amortized over the estimated useful life of the
system. In 1997, expenses incurred by the Company for these evaluation programs
were not material. However, due to the positive test results in the diesel
engine emissions program, the Company anticipates that more extensive
development and engineering will be needed in order to commercialize its
technology for such use. There can be no assurance as to the outcome of such
evaluation programs or, if initiated, the outcome of any such applications
development and engineering effort.

RESULTS OF OPERATIONS
---------------------

Revenues were $2.8 million and $5.7 million for the three months and six months
ended June 30, 1998, up from $2.3 million and $3.3 million for the three months
and six months ended June 30, 1997. The increase in revenues was primarily
attributable to sales of large FTO systems to customers overseas, primarily in
the United Kingdom, and an increase in domestic activity. Significant customers
accounted for 43% and 29%, respectively, of revenues in the three months ended
June 30, 1998, and 38% and 18%, respectively, of revenues in the six months
ended June 30, 1998. Revenues from international customers for the three months
and six months ended June 30, 1998 were 53% and 54%, respectively, compared to
48% and 42%, respectively, of revenues for the three months and six months ended
June 30, 1997.

The Company had a gross margin contribution of $176,000 and $531,000,
respectively, in the three months and six months ended June 30, 1998 compared to
gross margin losses of $233,000 and $555,000, respectively, in the comparable
periods in 1997. The increase in gross margin was primarily attributable to
higher revenues, which were sufficient to absorb the fixed and semi-fixed costs
of engineering and operations in the United States and Europe, and to a lesser
extent, reductions in costs from repeat sales of systems for established
applications.

Research and development expenses were $407,000 and $662,000, respectively, in
the three months and six months ended June 30, 1998, compared to $437,000 and
$620,000, respectively, for the comparable periods in 1997. Research and
development expenses were largely attributable to expenditures for the
development and testing of a prototype system utilizing the Company's patented
FTO technology for the treatment of diesel engine emissions from mobile sources,
the development of a prototype of a new FTO configuration, and PADRE(R) product
development.

Selling, general and administrative expenses decreased to $1.4 million and $2.9
million, respectively, for the three months and six months ended June 30, 1998,
compared to $1.8 million and $3.4 million, respectively, in the comparable
periods in 1997. The decrease in selling, general and administrative expenses
reflects reduced staffing and related costs, lower sales commissions and
marketing expenses, and a decrease in travel expenses, partially offset by
higher consulting and legal fees.

Net interest income of $105,000 and $210,000 for the three months and six months
ended June 30, 1998 primarily results from the investment of the net proceeds
from the Company's initial public offering completed in June 1996.

                                       9
<PAGE>
 
LIQUIDITY AND CAPITAL RESOURCES
-------------------------------

Total cash and short-term investments were $6.1 million at June 30, 1998, down
from $7.6 million at December 31, 1997. This decrease was primarily due to cash
used in operations. Net cash used in operating activities was $1.4 million in
the six months ended June 30, 1998, compared to $3.5 million used in operating
activities during the six months ended June 30, 1997. The reduction in cash used
in operating activities is primarily a result of reduced operating losses and an
increase in accounts payable and billings on uncompleted contracts in excess of
costs, partially offset by an increase in accounts receivable. The increases in
accounts payable and accounts receivable are primarily attributable to the
increase in revenue.

The Company has a $4.0 million accounts receivable line of credit with a
$2,000,000 letter of credit sub-limit. The committed line will bear interest at
the prime interest rate plus 0.50% and is subject to certain financial and non-
financial covenants. There are no interest-bearing borrowings outstanding under
the line of credit as of June 30, 1998. The Company has a stand-by letter of
credit issued under the sub-facility in the amount of $282,000. The Company
anticipates satisfying its remaining 1998 cash requirements from, among other
things, (i) its cash and short-term investments, (ii) increased revenues and
positive gross margin, (iii) the timely collection of accounts receivable, and
(iv) the line of credit facility. These strategies are dependent on the
Company's ability to continue to meet its forecasts, including developing
increased sales and generating positive gross margins therefrom, the timely
collection of amounts due to the Company and compliance with the line of credit
agreement covenants. The Company believes that its existing cash and short-term
investments and line of credit facility will provide sufficient liquidity for it
to meet its obligations throughout 1998.

YEAR 2000 COMPLIANCE
--------------------

The Year 2000 issue arises from computer programs that use two digits rather
than four to define the applicable year. Such computer programs may cause
computer systems to recognize a date using "00" as the calendar year 1900 rather
than the calendar year 2000. Systems that do not properly recognize such
information could generate erroneous dates or cause a system to fail.

The Company has conducted a preliminary review of its products and internal
computer systems to identify the systems that could be affected by the Year 2000
issue. A more comprehensive review will be completed by the end of 1998. The
Company believes its products and most of its management information systems are
already Year 2000 compliant, however its existing accounting system is not. The
Company plans to upgrade to a Year 2000 compliant version of its accounting
system by the end of 1998 and does not anticipate that the cost of such a
conversion will be material.

While the Company currently expects the Year 2000 issue will not pose
significant operational problems, failure to fully identify all Year 2000
dependencies in the Company's systems could have a material adverse effect on
the Company's business, results of operations and financial condition. In
addition, the Company cannot be sure that systems of other companies on which
the Company relies will be converted in a timely manner. The failure of other
companies to convert systems on which the Company relies may have a material
adverse effect on the Company's business, results of operations or financial
condition.

CERTAIN BUSINESS CONSIDERATIONS
-------------------------------

The Company's business is subject to the following risks and uncertainties, in
addition to those described elsewhere.

                                       10
<PAGE>
 
Operating Losses and Accumulated Deficit; Uncertainty of Future Profitability.
The Company had a net loss of approximately $9.6 million in 1997 and $2.8
million for the six months ended June 30, 1998, and had an accumulated deficit
of approximately $39.5 million at June 30, 1998. The Company does not expect to
be profitable unless and until sales of its systems generate sufficient revenues
with an appropriate gross margin to fund its operations. In the event the
Company does not achieve such revenues or margins, the Company may require
additional financing to fund its operations in the future. There can be no
assurance that such financing will be available or, if available, that it will
be on favorable terms.

Ability to Compete Against Lower Cost Technologies. To date, FTO systems have
been installed in a small segment of a number of industries. There can be no
assurance that the Company's FTO technology will receive broad market acceptance
as an economically and environmentally acceptable means of destroying VOCs. The
Company's ability to compete will depend upon the Company's ability to persuade
potential customers to adopt its FTO technology in place of certain, more
established, competing technologies, including flame-based destruction and
carbon adsorption systems. The failure of the Company to persuade a significant
number of potential customers to adopt its FTO technology would have a material
adverse effect on the growth of the Company's business, results of operations
and financial condition.

Sensitivity to Major Projects. For the six months ended June 30, 1998, two
projects accounted for 55% of the Company's revenues. In 1997, two projects
accounted for 38% of the Company's revenues and in 1996, three projects
accounted for 38% of the Company's revenues. Although the Company is expanding
the number of its customers and installations, the average size and dollar
volume of each installation has been increasing. The Company anticipates the
size of turnkey projects in 1998 will range from $1 million to $4 million, up
from an average of $850,000 in 1996. As a result, the Company's results of
operations are likely to continue to be dependent on major projects. Such a
reliance on major orders is likely to lead to fluctuations in quarterly results.

Larger projects also pose other challenges. The sales cycle for larger projects
tends to be longer than for smaller projects, and, when orders are received,
projects may be delayed by factors outside the Company's control, including
customer budget decisions, design changes and delays in obtaining permits.
Orders for large systems are often issued in stages and it is not uncommon for
there to be delays between the completion of the engineering design phase and
the receipt of the equipment order due to complex permitting and/or other
requirements. In addition, orders for large systems often have tight delivery
schedules and the customer will often attempt to negotiate penalties for late
delivery and/or the ability to assess liquidated damages for lost production if
the delivery schedule is not met. Also, because the dollar volumes are larger,
the costs of providing warranty services could increase. The Company's business,
results of operations and financial condition could be materially adversely
affected if the Company were to fail to obtain major project orders, if such
orders were delayed, if installations of such systems were delayed, or if such
installations encountered operating, warranty or other problems.

Management of Growth. Although it relies on subcontractors to fabricate
subassemblies and to assemble and install completed systems, the Company uses
its own employees to design, test and commission systems. The Company seeks to
maintain engineering and design staffing levels adequate for current and near-
term demand. During periods of rapid growth, such as that experienced by the
Company during 1996 and 1998, the Company's engineering and design personnel
generally operate at full capacity. As a result, future growth, if any, is
limited by the Company's ability to recruit and train additional engineering,
design and project management personnel and by the ability and performance of
the individual employees in managing more and larger projects. Furthermore, any
failure to maintain quality or to meet customer installation schedules could
damage relationships with important customers, damage the Company's reputation
generally and result in contractual liabilities. There can be no assurance that
the Company will be able to effectively manage an expansion of its operations or
that the

                                       11
<PAGE>
 
Company's systems or controls will be adequate to support the Company's
operations if expansion occurs. In such event, any failure to manage growth
effectively could have a material adverse effect on the Company's business,
results of operations and financial condition.

Risks Associated with International Operations and Sales. In 1997, sales to
international customers in Europe and Asia increased to 35%, up from 14% in
1996. For the six months ended June 30, 1998, sales to international customers
in Europe increased to 53%. The Company plans to increase its revenues, in part,
through an expansion of its overseas operations. Expansion internationally
encompasses the need to provide an infrastructure for operations, sales and
administration. The Company's overseas growth has placed, and could continue to
place, a significant strain on its managerial, operational and financial
resources. There can be no assurance that the Company will be able to attract,
hire and train personnel or to continue to develop the infrastructure needed on
a timely basis which may have an adverse impact on the Company's business,
results of operations and financial condition.

Additionally, the Company's business, results of operations and financial
condition may be materially adversely affected by fluctuations in currency
exchange rates and duty rates, and therefore its ability to maintain or increase
prices due to competition. The Company denominates international sales in either
United States dollars or local currencies. Sales in Europe have been primarily
denominated in pounds sterling. Since some expenses in connection with
international contracts are often incurred in foreign currency, there can be a
short-term exchange risk created. If the Company has significant international
sales or purchases in the future denominated in foreign currencies, the Company
may purchase hedging instruments to mitigate the exchange risk on these
contracts.

Risks Associated with Fixed Price Contracts. A majority of the Company's
contracts are performed using "fixed-price" rather than "cost-plus" terms. Under
fixed-price terms, the Company quotes firm prices to its customers and bears the
full risk of cost overruns caused by estimates that differ from actual costs
incurred or manufacturing delays during the course of the contract. Some costs,
including component costs, are beyond the Company's control and may be difficult
to predict. If manufacturing or installation costs for a particular project
exceed anticipated levels, gross margins would be materially adversely affected,
and the Company could experience losses. In addition, the manufacturing process
may be subject to significant change orders. However, in some cases the cost of
these change orders may not be negotiated until after the system is installed.
The failure of the Company to recover the full cost of these change orders could
materially adversely affect gross margins and also cause the Company to
experience losses.

Dependence on Key Personnel. The Company's success depends to a significant
extent upon its executive officers and key engineering, sales, marketing,
financial and technical personnel, both in the United States and overseas.
Employees may voluntarily terminate their employment with the Company at any
time, and none of the Company's employees is subject to any term employment
contract with the Company. The Company has limited personnel resources available
to address the different activities in its business. The loss of the services of
one or more of the Company's key employees could have a material adverse effect
on the Company's business, results of operations and financial condition.

The Company also believes that its future success will depend in large part upon
its ability to attract and retain additional highly skilled personnel,
particularly design and process engineers. Because of the technical
sophistication of the Company's systems and the sophisticated engineering
software utilized by the Company, design and process engineers who join the
Company generally are required to have advanced technical knowledge and
significant training to perform efficiently and productively. The availability
of such personnel is limited, and the Company has at times experienced
difficulty in locating new employees with the requisite level of expertise and
experience. In addition, the Company believes its ability to manage the
anticipated increase in customer orders for the Company's products in Europe
will depend in a large part on its success in attracting and retaining skilled
project managers and

                                       12
<PAGE>
 
engineers in Europe. There can be no assurance that the Company will be
successful in retaining its existing key personnel or in attracting and
retaining the personnel it requires in the future.

The Company maintains key employee life insurance on the life of its Chairman,
President and Chief Executive Officer, John T. Schofield, in the amount of
$2,000,000. There can be no assurance that such amount will be sufficient to
compensate the Company for the loss of the services of such individual.

Fluctuations in Quarterly Operating Results. The Company's quarterly revenues
and operating results have varied significantly in the past and may fluctuate
significantly in the future as a result of a variety of factors, many of which
are outside the Company's control. Such factors include the size and timing of
individual orders, the timing and amount of project change orders, customer
delays, order cancellations, general economic and industry conditions, the
amount of first-time engineering needed, the introduction of new products or
services by the Company or its competitors or the introduction of the Company's
products to new markets, changes in the levels of operating expenses, including
development costs, and the amount and timing of other costs relating to the
expansion of the Company's operations.

Furthermore, the purchase of the Company's products, particularly for major
projects, may involve a significant commitment of capital, with the attendant
delays frequently associated with large capital expenditures and authorization
procedures within its customers' organization. For these and other reasons, the
sales cycle for the Company's products can be lengthy (up to two years) and
subject to a number of significant risks over which the Company has little or no
control, including customer budgetary constraints. The Company historically has
operated with little backlog because most customer orders are placed with
relatively short lead times, usually from four to thirty weeks. Variations in
the timing of recognition of specific revenues due to changes in project scope
and timing may adversely and disproportionately affect the Company's operating
results for a quarter because the Company establishes its expenditure levels on
the basis of expected future revenues, and a significant portion of the
Company's expenses do not vary with current revenues.

Risks Associated With the Diesel Engine Emission Control Development Program.
The engineering challenges involved in treating diesel emissions are different
in a number of respects from the conditions in which the Thermatrix technology
has been used in the past, and there can be no assurance that it will prove
successful in this development area. Moreover, the Company's extensive database
of test results that it uses to design systems for industrial installations may
not be relevant to diesel engine emission control. Although the results of its
recently completed technology evaluation program were positive, the Company
anticipates that more extensive development and engineering will be needed in
order to commercialize the technology for such use. The level of expenditure by
the Company in this area will depend on the degree of support it receives from
strategic partners. Although pilot test results to date have been positive,
there can be no assurance as to the success of any such effort.

                                       13
<PAGE>
 
PART II        OTHER INFORMATION

Item 1.  Legal Proceedings

From time to time, the Company has been, or may become, involved in litigation
proceedings incidental to the conduct of its business.  The Company does not
believe that any such proceedings presently pending will have a material adverse
effect on the Company's financial position or its results of operations.

ITEM 2.  CHANGES IN SECURITIES

Not applicable.

ITEM 3.  DEFAULTS UPON SENIOR SECURITIES

Not applicable.

ITEM 4.  SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS

On June 11, 1998, the annual meeting of stockholders of the Company was held in
San Jose, California.  The matters voted upon at the meeting and the results of
those votes were as follows:

1. Election of Class II Directors

                                          Votes
                              ----------------------------
                                 For     Withheld  No Vote
                              ---------  --------  -------
      Harry J. Healer, Jr.    6,727,701    12,339  901,802
      Charles R. Kokesh       6,734,091     5,949  901,802
      John M. Toups           6,734,091     5,949  901,802

      The terms of the following Class I and Class III directors continued after
   the meeting:  Robi Blumenstein, Rebecca P. Mark, Frank R. Pope, John T.
   Schofield and James M. Strock.  On June 17, Ms. Mark tendered her resignation
   from the Board.  On June 22, 1998, Joseph W. Sutton was elected to the Board,
   filling the vacancy created by Ms. Mark's resignation.

2. Amendment to the Employee Stock Purchase Plan to increase the number of
   shares of Common Stock reserved thereunder by 100,000 shares to 133,086
 
                        For     Against  Abstain  No Vote
                     ---------  -------  -------  -------
                     6,698,355   30,185   11,500  901,802

3. Ratification of the appointment of Arthur Andersen LLP as independent public
   accountants


                        For     Against  Abstain  No Vote
                     ---------  -------  -------  -------
                     6,729,960    3,150    6,930  901,802

ITEM 5.  OTHER INFORMATION

In June 1996, the Company completed an initial public offering and raised net
proceeds of $22.1 million.  All of  the proceeds of the initial public offering
had been used as of June 30, 1998.  The proceeds were used for the repayment of
short-term borrowings, immediately following the initial public offering, and to
fund operations.

                                       14
<PAGE>
 
ITEM 6.  EXHIBITS AND REPORTS ON FORM 8-K.

(a)   Exhibits

      3.3   Restated Certificate of Incorporation of Registrant.(**)
      3.4   Amended and Restated Bylaws of Registrant.(*)           
      4.2   Amended and Restated Investor Rights Agreement.(*)      
      10.1  Form of Indemnification Agreement between the Registrant and each 
            of its directors and executive officers.(*)
      10.2  1987 Incentive Stock Plan, as amended and related agreements.(*)
      10.3  1996 Stock Plan and form of Stock Option Agreement thereunder.(*)
      10.4  Employee Stock Purchase Plan and forms of agreement thereunder.(*)
      10.5  1996 Director Option Plan and form of Director Stock Option
            Agreement thereunder.(*)
      10.6  Asset Purchase Agreement between the registrant and Purus, Inc.
            dated January 4, 1996.(*)
      10.7  Lease dated June 12, 1995 between the Registrant and Spieker
            Properties, L.P., as amended.(*)
      10.8  Lease dated June 24, 1995 between the Registrant and American
            General Life Insurance Company.(*)
      10.11 Amended and Restated Loan and Security Agreement between the
            Registrant and Venture Banking Group, a Division of Cupertino
            National Bank, dated January 21, 1998.(***)
      10.12 1996 Stock Plan:  UK Rules for Employees.(***)
      10.13 First Amendment to the Amended and Restated Loan and Security
            Agreement between Registrant and Venture Banking Group, a Division
            of Cupertino National Bank.(***)
      27.1  Financial Data Schedule.

      _______________
       (*)  Incorporated by reference to exhibits filed with the Registrant's
            Registration Statement on Form S-1 (No. 333-4370) which became
            effective June 19, 1996.
      (**)  Incorporated by reference to exhibits filed with the Registrant's
            Quarterly Report on Form 10-Q for the quarter ended September 30,
            1997.
     (***)  Incorporated by reference to exhibits field with the Registrant's
            Annual Report on Form 10-K for the year ended December 31, 1997.

(b)   Reports on Form 8-K

None

TRADEMARK ACKNOWLEDGMENTS

 .  Thermatrix and PADRE are registered trademarks of the Company.

                                       15
<PAGE>
 
                                   SIGNATURE

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



                                  THERMATRIX INC.



Date: August 14, 1998             By: /s/ Daniel S. Tedone
                                     ________________________________________
                                     Daniel S. Tedone
                                     Executive Vice President and
                                     Chief Financial Officer
                                     (Principal Financial and Accounting
                                     Officer)



                                  By: /s/ Barbara E. Krimsky
                                     ________________________________________
                                     Barbara E. Krimsky
                                     Vice President, Administration

                                       16