<PAGE>   1

                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549
                                    FORM 10-K


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

For the fiscal year ended June 30, 1999

[ ] 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 0-15383

                                 CEM CORPORATION
--------------------------------------------------------------------------------
             (Exact name of Registrant as specified in its charter)

         North Carolina                               56-1019741
    ------------------------            ------------------------------------
    (State of Incorporation)            (I.R.S. Employer Identification No.)

                    3100 Smith Farm Road, Matthews, NC 28104
--------------------------------------------------------------------------------
                    (Address of principal executive offices)

               Post Office Box 200, Matthews, North Carolina 28106
--------------------------------------------------------------------------------
                (Mailing address of principal executive offices)

Registrant's telephone number, including area code:  (704) 821-7015

Securities Registered Pursuant to Section 12(b) of the Act:  NONE
Securities Registered Pursuant to Section 12(g) of the Act:

                           $.05 par value Common Stock
                           ---------------------------
                                (Title of Class)

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 [ ]

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405
of Regulation S-K is not contained herein, and will not be contained, to the
best of Registrant's knowledge, in definitive proxy or information statements
incorporated by reference in Part III of this Form 10-K or any amendment to this
Form 10-K. [ ]

The aggregate market value of shares of the Registrant's $.05 par value Common
Stock, its only outstanding class of voting stock, held by non-affiliates as of
September 8, 1999, was $17,179,844 assuming, for purposes of this filing, that
all executive officers and directors of the Registrant are affiliates. The
number of issued and outstanding shares of the Registrant's $.05 par value
Common Stock, its only outstanding class of Common Stock, as of September 8,
1999, was 3,043,443 shares.

Portions of the CEM Corporation Annual Report to Shareholders for the fiscal
year ended June 30, 1999 are incorporated by reference into Parts I and II.
Portions of the Proxy Statement for the Annual Meeting of Shareholders to be
held November 4, 1999 are incorporated by reference into Part III.


<PAGE>   2


PART I

ITEM 1 - BUSINESS

General

     CEM Corporation (the "Company") engages in one line of business, the
development, manufacture, sale and service of microwave-based instrumentation
for testing, analysis and process control in analytical laboratory and
industrial markets. These sample preparation products provide advantages of
speed and simplicity compared to traditional methods of testing and analysis.
The Company's products are used in the general analytical laboratory market and
in many manufacturing and processing industries, including chemical and food
processing. A significant amount of the Company's sales consists of consumable
supplies, parts and service for its instrumentation. The Company was organized
as a North Carolina corporation in 1971.

Products

     Microwave Accelerated Reaction System("MARS") and Microwave Digestion
System("MDS"). MARS and MDS and related accessories accounted for approximately
36%, 33%, and 29% of the Company's consolidated sales in fiscal 1999, 1998 and
1997, respectively. This product is a microwave heating system designed
especially for use in the digestion of samples for laboratory analysis. It
performs a rapid dissolution of samples in acid in a closed vessel system and is
sold to the analytical laboratory market. MARS, which was introduced in the
first quarter of fiscal 1998 and is the next generation of MDS, permits higher
pressures to be used safely and provides greater measurement data for control of
the instrument.

     Moisture/Solids Analyzer. The Moisture/Solids Analyzer and related
accessories accounted for approximately 20%, 17% and 19% of the Company's
consolidated sales in fiscal 1999, 1998 and 1997, respectively. This product
performs percent moisture or percent solids measurement in process control
monitoring, quality control and product development in a variety of industries,
including chemical processing, pharmaceuticals, food and dairy products,
tobacco, textiles, paint and coatings, pulp and paper, water and wastewater
treatment.

     Microwave Ashing System. The Microwave Ashing System uses microwave energy
to rapidly oxidize a sample to determine the ash (metal oxide) content. This
product is primarily sold to the analytical laboratory market and petrochemical
industry.

     STAR System. The STAR system, which incorporates temperature control and
reagent (acid) addition, is an open cavity microwave heating system designed
initially for use in the digestion of samples for laboratory analysis. It
performs a rapid dissolution of samples and is sold to the food, polymer,
petroleum, chemical and semi-conductor industries.

     Fat Analyzer System. The Company manufactures an automatic extraction unit
which is used in conjunction with the Moisture/Solids Analyzer to form the Fat
Analyzer System. This product measures the fat content of a variety of samples
and is sold primarily to meat processing and other food industries.

     ProFat II System. The ProFat II System, which was introduced in the first
quarter of fiscal 1998, is a microwave-based instrument that provides rapid
moisture, fat and protein results on most meat products, without solvents. The
product is sold primarily to companies processing beef, poultry and pork
products that require a rapid result for process control purposes and companies
which utilize non solvent-based instruments for product analysis.

     Microwave Extraction System. The Microwave Extraction System uses microwave
energy to rapidly heat solvents to high temperatures. These elevated
temperatures reduce the time necessary to extract organic compounds from solid
matrices. This product uses a unique temperature control system and multiple
safety devices to ensure both rapid and safe sample preparation. This product is
a cost effective alternative to traditional solvent extraction due to its high
recoveries and significantly reduced solvent usage. The Microwave Extraction
System is marketed under the trade name, MARS-X. Sales of the MARS-X to
environmental laboratories will be limited in the United States until the U.S.
Environmental Protection Agency approves the use of microwave-based instruments
as an alternative method for extraction.


                                       2
<PAGE>   3


Marketing and Sales

     The Company's marketing and sales strategy is based on identifying
applications for its products and providing its customers with prompt and
effective technical and applications support.

     The Company's marketing strategy utilizes telemarketing, direct mail, trade
show demonstrations, articles, studies, trade journal advertising, product
releases, seminars and makes extensive use of the Company's applications
laboratory to develop specific testing applications for potential and existing
customers.

     Sales in the U.S. are generated by full-time sales personnel through sales
and service locations throughout the country. Sales are conducted through direct
selling efforts including on-site demonstrations. Sales and service
representatives provide installation and training of production and laboratory
personnel. Sales representatives are paid a base salary, commissions and/or
other incentive compensation.

     The Company's applications laboratories provide technical assistance to
customers and potential customers in developing new and improved applications
and related procedures. The applications laboratories perform tests in its
facilities in North Carolina and Germany and provides the results to customers.

     The Company's foreign sales are conducted through independent dealers
throughout the world and the Company's subsidiaries in England, Germany and
Italy. Foreign sales are primarily to customers in Europe, Asia and Latin
America. Foreign sales accounted for 43%, 45% and 46% of net sales in fiscal
1999, 1998 and 1997, respectively.

Research and Development

     The Company invests heavily in the research and development of potential
new products, product improvements and enhancements, and applications research
for existing products. For fiscal 1999, 1998 and 1997, research and development
expense was $3,162,000, $2,943,000 and $2,742,000 respectively.

     The Company's product development efforts continue to progress with respect
to certain proprietary technology licensed in 1996. The Company expects to
deliver prototype instruments incorporating this technology to prospective
customers in fiscal 2000.

Product Protection

     The Company relies upon its proprietary technology, continuing research and
development and customer service support to maintain and enhance its competitive
position. Important features of certain of the Company's products are protected
by issued patents or pending patent applications.

Manufacturing

     The Company's manufacturing operations are carried out at its headquarters
in Matthews, North Carolina and consist mostly of the assembly and testing of
mechanical and electronic components purchased from others.

     Certain components are currently purchased from single source suppliers. An
interruption of one of these sources could result in delays in the Company's
production while the Company developed an alternative supplier and could result
in a loss of sales and income. There are other single source components for
which the Company has determined that other sources are readily available.

     The Company has experienced no significant production delays because of a
supplier's inability to ship an acceptable component. The Company stocks what it
believes is an adequate supply of all components and materials based upon
delivery lead times and orders currently in hand.

Environmental Regulations

     Compliance with federal, state and local provisions relating to protection
of the environment has not had, and is not expected to have, any material
adverse effects upon the production, capital expenditures, earnings or
competitive position of the Company and its subsidiaries.


                                       3
<PAGE>   4


Employees

     At June 30, 1999, the Company employed 179 persons. None of the Company's
employees are covered by a collective bargaining agreement.

Backlog

     The Company does not have a significant backlog of orders, as it normally
ships its products within a short time after it receives orders.

Competition

     The Company experiences direct competition in both foreign and U.S. markets
from companies using microwave technology, traditional methods of heating and
drying and other technologies.

     There are a number of methods for performing acid digestions, the most
common of which is the traditional "open vessel on a hot plate" method. There
are three other primary manufacturers of closed vessel microwave digestion
systems similar in nature to the Company's products. Also competing with MARS
and MDS are other advanced methods utilizing higher pressure and temperature
including steel jacketed digestion vessels for use in conventional ovens and
high pressure wet ashers.

     There are a number of other methods for testing the moisture or solids
content of various liquids and solids. In most instances, the equipment and
instruments, which consist typically of simple heating and drying units and
measurement techniques, are less expensive than the Moisture/Solids Analyzer
produced by the Company. In addition, infrared moisture analyzers, radio
frequency energy absorption techniques and the Karl Fischer titration method, a
wet chemical procedure, have been developed. These systems compete directly with
the Company's instrumentation in certain markets. There is one manufacturer of a
microwave moisture system similar in nature to the Company's Moisture/Solids
Analyzer.

     The traditional method of ashing is with a resistance heat furnace. There
are a number of manufacturers of laboratory furnaces used for ashing. Although
these products are typically less expensive than the Microwave Ashing System
sold by the Company, the Company's product offers advantages in both speed and
process control.

     The Company's microwave open vessel digestion system (the STAR System) is
designed to digest large samples or samples that are very reactive and can not
be safely digested in a closed vessel digestion system. There is currently one
competitor in this market, which also utilizes microwave based technology and
automatic reagent additions, but the Company believes its product offers
advantages in price and performance.

     The Company's Fat Analyzer System is the only direct moisture, fat and
protein system available that is approved by the Association of Analytical
Chemists. However, there is a competing technology using an indirect measurement
method of analysis, which results in a quicker result time but is not considered
as accurate. In addition, this competing system is sold at a significantly
higher price than the Company's system.

     There are a number of methods for performing extractions, the most common
of which are the traditional Soxhlet and sonication methods. Also competing with
the Company's Microwave Extraction System are other advanced methods such as
Supercritical Fluid Extraction and Accelerated Solvent Extraction.

     Typically the Company's selling prices are higher than those of most of its
competitors. The Company competes primarily upon the speed, ease of use,
applications support and long-term cost savings to the users.

International Operations and Sales

     Information about the Company's international operations and sales is
incorporated by reference to footnotes 1 and 8 of the financial statements
contained in the Company's 1999 Annual Report to Shareholders (Exhibit 13
hereto).


                                       4
<PAGE>   5


ITEM 2 - PROPERTIES

     The Company's headquarters, research and manufacturing operations are
located in an 82,000 square foot building on an eight and three-fourths acre
tract of land owned by the Company in Matthews, North Carolina. The Company also
owns a 5,000 square foot office and warehouse facility in England, owns a 5,200
square foot office and warehouse in Germany and leases a 4,000 square foot
office in Italy. The facility in Germany is subject to a mortgage which had a
balance of $68,000 at June 30, 1999. Management believes these facilities are
adequate to serve existing markets for the next several years.

ITEM 3 - LEGAL PROCEEDINGS

     Nothing is required to be disclosed pursuant to this item.


ITEM 4 is inapplicable and has been omitted.


PART II

ITEM 5 is incorporated by reference to Footnote 12 on page 19 "Quarterly
Information (Unaudited)" and on the inside back cover "Corporate Information" of
the Registrant's 1999 Annual Report to Shareholders (Exhibit 13 hereto).

ITEM 6 is incorporated by reference to page 20 of items captioned "Selected
Financial Data" of the Registrant's 1999 Annual Report to Shareholders (Exhibit
13 hereto).

ITEM 7 is incorporated by reference to page 6 captioned "Management's Discussion
and Analysis" of the Registrant's 1999 Annual Report to Shareholders (Exhibit 13
hereto).

ITEM 7A is incorporated by reference to Footnote 2 on page 14 "Financial
Instruments" of the Registrant's 1999 Annual Report to Shareholders (Exhibit 13
hereto).

ITEM 8 - FINANCIAL STATEMENTS AND SUPPLEMENTARY DATA

     The financial statements, notes to the financial statements and quarterly
supplemental financial data of the Company appearing on pages 9 - 20 of the
Company's 1999 Annual Report to Shareholders are hereby incorporated by
reference.

ITEM 9 is inapplicable and has been omitted.

PART III

ITEM 10 - DIRECTORS AND EXECUTIVE OFFICERS OF THE REGISTRANT

     Information as to the directors and chief executive officer of the Company
is incorporated herein by reference to the section captioned "Election of
Directors" of the Company's Proxy Statement for the Annual Meeting of
Shareholders to be held November 4, 1999. The following information is provided
as to the executive officers of the Company who are not directors:

Name                   Age          Background
---------------------  ------       --------------------------------------------

Richard N. Decker      50           Vice President - Finance, Chief Financial
                                    Officer, Secretary and Treasurer since 1995;
                                    Secretary, Treasurer and Chief Financial
                                    Officer 1993-1995; Vice President-Finance of
                                    the Water and Gas Meter Division of
                                    Schlumberger Limited Corporation 1982-1993.

     All of the Company's executive officers were appointed to their current
positions at the Annual Meeting of the Board of Directors held on November 5,
1998. All of the Company's executive officers' terms of office extend until the
next Annual Meeting of the Board of Directors and until their successors are
elected and qualified.

ITEM 11 is incorporated by reference to the sections captioned "Executive
Compensation" and "Director Compensation" in the Registrant's Proxy Statement
for Annual Meeting of Shareholders to be held November 4, 1999.


                                       5
<PAGE>   6


ITEM 12 is incorporated by reference to the sections captioned "Principal
Shareholders and Holdings of Management" and "Section 16(a) Beneficial Ownership
Reporting Compliance" in the Registrant's Proxy Statement for Annual Meeting of
Shareholders to be held November 4, 1999.


ITEM 13 is inapplicable and has been omitted.

PART IV

ITEM 14 - EXHIBITS, FINANCIAL STATEMENT SCHEDULES AND REPORTS ON FORM 8-K

(a)  (1) Financial Statements. See accompanying Index to Financial Statements.
     (2) Financial Statement Schedules. See accompanying Index to Financial
         Statements.
     (3) Exhibits.

               3.1         Restated Charter of the Company, as amended.(1)

               3.2         Bylaws of the Company.(1)

               10.1    *   CEM Corporation 1986 Nonqualified Stock Option Plan,
                           as amended, incorporated herein by reference to the
                           Company's Registration Statement on Form S-8 (File
                           No. 33-53694).

               10.2    *   CEM Corporation Employee Stock Purchase Plan, as
                           amended, incorporated herein by reference to the
                           Company's Registration Statement on Form S-8 (File
                           No. 33-80136).

               10.3    *   CEM Corporation 1987 Stock Option Plan, as
                           amended.(1)

               10.4    *   CEM Corporation 1993 Management Equity Plan,
                           incorporated herein by reference to the Company's
                           Registration Statement on Form S-8 (File No.
                           33-75368).

               10.5    *   CEM Corporation Management Incentive Compensation
                           Plan(2).

               10.6        CEM Corporation 1993 Nonqualified Stock Option Plan
                           for Non-Employee Directors, incorporated herein by
                           reference to the Company's Registration Statement on
                           Form S-8 (File No. 33-75366).

               13.         The Company's 1999 Annual Report to Shareholders.
                           This Annual Report to Shareholders is furnished for
                           the information of the Commission only and, except
                           for the parts thereof incorporated in this report, is
                           not deemed to be "filed" as part of this filing.

               21.         List of the Company's Subsidiaries.(1)

               23.         Consent of Independent Accountants.

               27.         Financial Data Schedules (filed in electronic format
                           only). This schedule shall not be deemed "filed" for
                           purposes of Section 11 of the Securities Act of 1933
                           or Section 18 of the Securities Exchange Act of 1934
                           or otherwise be subject to the liabilities of such
                           sections, nor shall it be deemed a part of any
                           registration statement to which it relates.

               99.         Revised Item 21 of Part II to the Company's
                           registration statements on Form S-8 (Registration
                           Numbers 33-11952 and 33-25739).(1)

               --------------------
                       *   This exhibit is one of the Company's management
                           contracts and compensatory plans and arrangements.
                      (1)  Incorporated herein by reference to the Company's
                           Form 10-K for the year ended June 30, 1994.
                      (2)  Incorporated herein by reference to the Company's
                           Form 10-K for the year ended June 30, 1997.


(b) Reports on Form 8-K. No reports on Form 8-K have been filed during the last
quarter of the period covered by this report.

(c) Exhibits. See Item 14(a)(3) above.



                                       6
<PAGE>   7


<TABLE>
<CAPTION>
                                                                                       Reference (Page)
                                                                              -----------------------------------

                                                                                                        Annual
                                                                                Form 10-K              Report to
Item 14. (d) Index to Financial Statements and Schedules                      Annual Report          Shareholders
--------------------------------------------------------------------------    -------------          ------------
<S>                                                                           <C>                    <C>

Data incorporated by reference from the attached
1999 Annual Report to Shareholders:

    Report of Independent Accountants                                                                     20

    Consolidated Balance Sheets as of June 30, 1999 and 1998                                               9

    Consolidated Statements of Income for the years ended                                                 10
    June 30, 1999, 1998 and 1997

    Consolidated Statements of Cash Flows for the years                                                   11
    ended June 30, 1999, 1998 and 1997

    Consolidated Statements of Changes in Shareholders' Equity for the                                    12
    years ended June 30, 1999, 1998 and 1997

    Notes to Consolidated Financial Statements                                                          13 - 20


Data submitted herewith:

    Report of Independent Accountants                                               8

    Financial Statement Schedule:
        Schedule II - Valuation and Qualifying Accounts                             10
</TABLE>


The 1999 Annual Report to Shareholders of CEM Corporation is not to be deemed
"filed" as part of this report except for those parts thereof specifically
incorporated herein by reference.


                                       7
<PAGE>   8


REPORT OF INDEPENDENT ACCOUNTANTS
ON FINANCIAL STATEMENT SCHEDULE

To the Board of Directors of CEM Corporation:

Our audits of the consolidated financial statements referred to in our report
dated July 21, 1999 appearing on page 20 of the 1999 Annual Report to
Shareholders of CEM Corporation (which report and consolidated financial
statements are incorporated by reference in this Annual Report on Form 10-K)
also included an audit of the financial statement schedule listed in Item
14(a)(2) of this Form 10-K. In our opinion, this financial statement schedule
presents fairly, in all material respects, the information set forth therein
when read in conjunction with the related consolidated financial statements.





/s/ PricewaterhouseCoopers  LLP



Charlotte, North Carolina
July 21, 1999


                                       8
<PAGE>   9


SIGNATURES


Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange
Act of 1934, the Company has duly caused this Annual Report to be signed on its
behalf by the undersigned, thereunto duly authorized.


                                    CEM CORPORATION

                                    By: /s/ Michael J. Collins
                                        ----------------------
                                        Michael J. Collins
                                        President and Chief Executive Officer

                                    By: /s/ Richard N. Decker
                                        ---------------------
Dated:  September 24, 1999              Richard N. Decker
                                        Chief Financial Officer, Secretary
                                        and Treasurer
                                        (Principal Financial and Accounting
                                        Officer)


Pursuant to the requirements of the Securities Exchange Act of 1934, this Annual
Report has been signed below by the following persons on behalf of the Company
and in the capacities and on the dates indicated.

<TABLE>
<CAPTION>
               Signature                                    Capacity                             Date
---------------------------------     -----------------------------------------------     ------------------
<S>                                   <C>                                                 <C>

/s/ Ronald A. Norelli                 Chairman of the Board of Directors                  September 24, 1999
---------------------------------
      Ronald A. Norelli

/s/ Michael J. Collins                President, Chief Executive Officer and Director     September 24, 1999
---------------------------------         (Principal Executive Officer)
      Michael J. Collins

/s/ John L. Chanon                    Director                                            September 24, 1999
---------------------------------
      John L. Chanon

/s/ George F. Krall                   Director                                            September 24, 1999
---------------------------------
      George F. Krall
</TABLE>


                                       9
<PAGE>   10


                                 CEM CORPORATION
                 SCHEDULE II - VALUATION AND QUALIFYING ACCOUNTS
                FOR THE YEARS ENDED JUNE 30, 1999, 1998 AND 1997



<TABLE>
<CAPTION>
                                                  Balance at
                                                  beginning of    Charged to costs                      Balance at
                          Description               period          and expenses       Deductions     End of period
                  ---------------------------     -----------     ----------------    ------------    -------------
<S>               <C>                             <C>              <C>                <C>             <C>

Year ended        Accounts receivable,            $ 1,019,000        $   360,000      $  (151,000)     $ 1,228,000
June 30, 1999     inventory and warranty
                  reserves

Year ended        Accounts receivable,              1,040,000            404,000         (425,000)       1,019,000
June 30, 1998     inventory and warranty
                  reserves

Year ended        Accounts receivable,            $   720,000        $   607,000      $  (287,000)     $ 1,040,000
June 30, 1997     inventory and warranty
                  reserves
</TABLE>


                                       10
<PAGE>   11


                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                                    EXHIBITS
                                  ITEM 14(a)(3)
                           ANNUAL REPORT ON FORM 10-K

For the Fiscal Year Ended                                Commission File Number
-------------------------                                ----------------------
      June 30, 1999                                              0-15383

                                 CEM CORPORATION
                                  EXHIBIT INDEX


Exhibit No.                Exhibit Description
-----------                -------------------

      3.1                  Restated Charter of the Company, as amended.(1)

      3.2                  Bylaws of the Company.(1)

      10.1                 CEM Corporation 1986 Nonqualified Stock Option Plan,
                              as amended, incorporated herein by reference to
                              the Company's Registration Statement on Form S-8
                              (File No. 33-53694).

      10.2                 CEM Corporation Employee Stock Purchase Plan, as
                              amended, incorporated herein by reference to the
                              Company's Registration Statement on Form S-8 (File
                              No. 33-80136).

      10.3                 CEM Corporation 1987 Stock Option Plan, as
                              amended.(1)

      10.4                 CEM Corporation 1993 Management Equity Plan,
                              incorporated herein by reference to the Company's
                              Registration Statement on Form S-8 (File No.
                              33-75368).

      10.5                 CEM Corporation Management Incentive Compensation
                              Plan.(2)

      10.6                 CEM Corporation 1993 Nonqualified Stock Option Plan
                              for Non-Employee Directors, incorporated herein by
                              reference to the Company's Registration Statement
                              on Form S-8 (File No. 33-75366).

      13.                  The Company's 1999 Annual Report to Shareholders.
                              This Annual Report to shareholders is furnished
                              for the information of the Commission only and,
                              except for the parts thereof incorporated in this
                              report, is not deemed to be "filed" as part of
                              this filing (page __ of the sequentially numbered
                              pages).

      21.                  List of the Company's Subsidiaries.(1)

      23.                  Consent of Independent Accountants (page __ of the
                              sequentially numbered pages).

      27.                  Financial Data Schedules (filed in electronic format
                              only). This schedule shall not be deemed "filed"
                              for purposes of Section 11 of the Securities Act
                              of 1933 or Section 18 of the Securities Exchange
                              Act of 1934 or otherwise be subject to the
                              liabilities of such sections, nor shall it be
                              deemed a part of any registration statement to
                              which it relates.

      99.                  Revised Item 21 of Part II to the Company's
                              registration statements on Form S-8 (Registration
                              Numbers 33-11952 and 33-25739).(1)

      ----------------------

                  (1) Incorporated herein by reference to the Company's Form
                      10-K for the year ended June 30, 1994.

                  (2) Incorporated herein by reference to the Company's Form
                      10-K for the year ended June 30, 1997.


                                       11