<PAGE>   1

                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                                   FORM 10-Q/A

                                 AMENDMENT NO. 1

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

                  FOR THE QUARTERLY PERIOD ENDED JUNE 30, 1999

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

                          Commission File No. 000-24769

                           CLARK/BARDES HOLDINGS, INC.
             (Exact Name of Registrant as Specified in its Charter)

               DELAWARE                                       52-2103926
   (State or Other Jurisdiction of                         (I.R.S. Employer
    Incorporation or Organization)                        Identification No.)

    2121 SAN JACINTO, SUITE 2200
           DALLAS, TEXAS                                       75201-7906
(Address of Principal Executive Offices)                       (Zip Code)

       Registrant's Telephone Number, Including Area Code: (214) 871-8717

         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 outstanding of the registrant's common stock, all
of which comprise a single class with a $0.01 par value, as of August 13, 1999,
the latest practicable date, was 9,628,749.


<PAGE>   2

         This Amendment No. 1 to Form 10-Q (the "Form 10-Q/A") amends and
supplements the quarterly report on Form 10-Q for the quarterly period ended
June 30, 1999, filed with the SEC on August 16, 1999 (the "Form 10-Q"), of
Clark/Bardes Holdings, Inc. Capitalized terms used herein have the meanings
ascribed to such terms in the Form 10-Q unless otherwise defined herein.

Note 2 to Item 1 of our Form 10-Q is amended to read as follows:

PART I. FINANCIAL INFORMATION

ITEM 1. FINANCIAL STATEMENTS


                   CLARK/BARDES HOLDINGS, INC. AND SUBSIDIARY
              NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS
                                  JUNE 30, 1999
                                   (UNAUDITED)

2. ACQUISITION OF MCG/HEALTHCARE

On April 5, 1999, CBI purchased the assets and business and assumed certain
liabilities of Phynque, Inc., d/b/a Management Compensation Group/HealthCare, a
Minnesota corporation, for a purchase price of $35.9 million consisting of:

         (i)      a cash payment of $13.8 million;

         (ii)     a promissory note for $8.7 million;

         (iii)    326,363 shares of common stock, having an aggregate value of
                  $5.3 million based on the closing price of the common stock on
                  April 5, 1999;

         (iv)     the direct payment of $3.6 million for certain outstanding
                  loans;

         (v)      the assumption of $4.2 million of liabilities and $310,000 of
                  closing costs.

The purchase price was determined by an arm's length negotiation among the
parties. The assets acquired include cash, receivables and operating assets in
addition to all intangible assets, intellectual property, files pertaining to
customers, computer software and systems and related licenses. The liabilities
assumed include commissions payable, accrued employee benefits and operating
expenses. The $17.4 million cash portion of the purchase price was funded by a
borrowing under CBI's existing credit facility. The promissory note is payable
in thirty-two equal quarterly installments of principal and interest at 10% per
annum of $430,000 commencing on April 5, 2000. The promissory note is secured by
a personal guarantee of W. T. Wamberg, Chairman of Clark/Bardes.

MCG/HealthCare is a 180 employee executive benefit consulting organization
servicing the healthcare industry. MCG/HealthCare is headquartered in
Minneapolis, Minnesota. Prior to the acquisition described above, there was no
material relationship between CBI and MCG/HealthCare.

The unaudited pro forma information below presents the results of CBI and
MCG/HealthCare as if the acquisition had occurred on January 1, 1998:


                                       2
<PAGE>   3

<TABLE>
<CAPTION>
                                            THREE MONTHS ENDED          SIX MONTHS ENDED
                                                 JUNE 30,                   JUNE 30,
                                           ---------------------      ---------------------
                                             1999         1998          1999         1998
                                           --------     --------      --------     --------
                                                            (IN THOUSANDS)
<S>                                        <C>          <C>           <C>          <C>
Pro forma:
     Revenues                              $ 29,714     $ 21,874      $ 59,534     $ 42,299
     Net income (loss)                     $  1,439     $ (5,386)     $  1,799     $ (5,170)

     Diluted earnings (loss) per share     $    .16     $  (1.58)     $    .20     $  (1.46)
</TABLE>


The following sections of Item 2 of our Form 10-Q are amended to read as
follows:

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

(Tables shown in Dollars in Millions, Except Per Share Amounts)



Management Compensation Group/HealthCare

On April 5, 1999, we purchased the assets and business and assumed certain
liabilities of Phynque, Inc., d/b/a Management Compensation Group/HealthCare for
a purchase price of $35.9 million consisting of the following:

     (1) a cash payment of $13.8 million;

     (2) a promissory note for $8.7 million;

     (3) 326,363 shares of common stock, having an aggregate value of $5.3
         million based on the closing price of the common stock on April 5,
         1999;

     (4) the direct payment of $3.6 million for certain outstanding loans; and

     (5) the assumption of $4.2 million of liabilities and payment of
         approximately $310,000 of closing costs.

The assets acquired included cash, receivables and operating assets in addition
to all intangible assets, and intellectual property. The liabilities assumed
included commissions payable, accrued employee benefits and operating expenses.
The $17.4 million cash portion of the purchase price was funded by a borrowing
under our existing credit facility. The promissory note is payable in thirty-two
equal quarterly installments of principal and interest at 10% per annum of
$430,000 starting April 5, 2000. The promissory note is secured by a personal
guarantee from W. T. Wamberg, Chairman of Clark/Bardes, Inc. MCG/Healthcare is a
180 employee executive benefit consulting organization servicing the healthcare
industry and is headquartered in Minneapolis, Minnesota.

The acquisition of MCG/Healthcare marked our entrance into the healthcare and
not-for-profit executive benefit and compensation plan business.

For the periods prior to the acquisition, MCG had revenue and net income as
follows:

<TABLE>
<CAPTION>
                                        FISCAL YEARS ENDED
         SIX MONTHS ENDED                 SEPTEMBER 30,
            MARCH 31,               --------------------------
              1999                    1998             1997
------------------------------      --------         --------
           (UNAUDITED)                       (AUDITED)
                                 (IN THOUSANDS)
<S>                   <C>           <C>              <C>
Revenue               $ 10,986      $ 26,000         $ 21,939
Net income (loss)     $ (1,696)     $  1,816         $    379
</TABLE>

MCG was an S corporation and, accordingly, did not pay federal income taxes.


                                       3
<PAGE>   4
The unaudited pro forma information below presents our results of operations and
that of MCG combined as if the acquisition had occurred on January 1, 1998.

<TABLE>
<CAPTION>
                                           THREE MONTHS ENDED          SIX MONTHS ENDED
                                                 JUNE 30,                   JUNE 30,
                                          ---------------------      ---------------------
                                            1999         1998          1999         1998
                                          --------     --------      --------     --------
                                                          (IN THOUSANDS)
<S>                                       <C>          <C>           <C>          <C>
Pro forma:
    Revenues                              $ 29,714     $ 21,874      $ 59,534     $ 42,299
    Net income (loss)                     $  1,439     $ (5,386)     $  1,799     $ (5,170)
    Diluted earnings (loss) per share     $    .16        (1.58)     $    .20        (1.46)
</TABLE>


Renewal Revenue

As in the case of first year revenue, the Clark/Bardes Division's bank-owned
life insurance revenue accounted for a significant percentage of our renewal
revenue:

     o    64.0% for the second quarter

     o    75.0% for the six month period - June 30, 1999 of our renewal revenue.

<TABLE>
<CAPTION>
 1999 - 1998         INCREASE
--------------       --------
<S>                  <C>       <C>
Second Quarter        $ 4.8     68.6%
Six Months            $ 8.2     54.3%
</TABLE>

The following table represents the gross revenue associated with our inforce
business-owned life insurance policies as of June 30, 1999. The projected gross
revenue stated below is not adjusted for mortality, lapse or other factors that
may impair the collection of revenue. For example, approximately $25.0 million
or 6.0% of the projected gross revenue is with General American. General
American is currently experiencing financial difficulties, and it is uncertain
that we can collect revenues associated with the policies placed with General
American, regardless of whether they remain inforce. We believe that the General
American revenues will be paid, however, we cannot assure you that commissions
associated with General American or any other insurance carriers that underwrite
these policies will be received.

                         PROJECTED GROSS INFORCE REVENUE
                                  JUNE 30, 1999

<TABLE>
<CAPTION>
                                BANK         HEALTHCARE
                CLARK       COMPENSATION    COMPENSATION
  YEAR          BARDES       STRATEGIES      STRATEGIES         TOTAL
  ----        ---------     ------------    ------------      ---------
<S>           <C>              <C>             <C>            <C>
  2000        $  40,342        $ 8,537         $ 7,864        $  56,743
  2001           37,806          4,573           7,828           50,207
  2002           36,037          3,348           7,689           47,074
  2003           33,388          3,418           7,572           44,377
  2004           29,538          3,457           7,292           40,287
  2005           29,054          3,497           6,885           39,436
  2006           29,008          3,539           6,550           39,097
  2007           27,044          3,584           6,214           36,842
  2008           24,957          3,629           5,499           34,085
  2009           22,208          3,676           4,663           30,547
              ---------        -------         -------        ---------
 Total        $ 309,382        $41,259         $68,054        $ 418,695
              =========        =======         =======        =========
</TABLE>

These projected gross revenues are based on the beliefs and assumptions of
management and are not necesssarily indicative of the revenues that may actually
be achieved in the future.

FINANCIAL CONDITION AND LIQUIDITY

We continue to generate strong cash flow from earnings. We use the net cash from
our operations and external financing to fund capital expenditures and small
acquisitions. While our current ratio was approximately one-to-one at June 30,
1999 compared to 1.6 to one at December 31, 1998, we believe that our strong
cash flow will be sufficient to fund capital requirements and all obligations as
they become due. We expect that large future acquisitions will be financed
primarily through externally available funds. However, we can offer no assurance
that such funds will be available and, if so, on terms acceptable to us.


                                       4
<PAGE>   5

<TABLE>
<CAPTION>
SIX MONTHS ENDED JUNE 30,       1999       1998      CHANGE
-------------------------      -----      -----      ------
<S>                            <C>        <C>        <C>
Cash flows from (used in):
   Operating activities        $ 8.0      $ 5.7      $ 2.3
   Investing activities        (41.6)      (1.5)     (40.1)
   Financing activities         31.8       (1.7)      33.5
</TABLE>


Cash Flows from Operating Activities

Our cash from operations improved during the first six months of 1999 compared
with the same period of 1998. The increased cash from operations consisted
primarily of two factors:

     o   Cash flow from earnings (net income plus non-cash charges) was $5.0
         million in 1999 compared with $5.6 million in 1998. However, it should
         be noted that no income taxes were paid in 1998; and

     o   Working capital contributed $3.0 million, primarily the result of
         timing of paying liabilities.

Cash Used in Investing Activities

Acquisitions accounted for $38.5 million of the $41.6 million used in investing
activities. The balance was comprised of $2.2 million for purchase of equipment
and $1.0 million for various non-current assets such as deferred debt expenses
($400,000) and artwork acquired in connection with the MCG Acquisition
($617,000).

Cash spending for acquisitions included:

     o        MCG/HealthCare                              $    17.4

     o        Assets from The Wamberg Organization        $     7.5

We expect acquisitions to continue for the remainder of the year and, which will
be financed primarily with cash available credit lines and possibly additional
equity. However, we can offer no assurances such will be the case.

CAUTIONARY STATEMENT CONCERNING FORWARD-LOOKING STATEMENTS

This Form 10-Q/A and the documents incorporated by reference in this Form 10-Q/A
may contain forward-looking statements within the meaning of Section 27A of the
Securities Act of 1933, as amended, and Section 21E of the Securities Exchange
Act of 1934, as amended. When used in this Form 10-Q/A, words such as
"anticipate," "believe," "estimate," "expect," "intend," "predict," "project,"
and similar expressions, as they relate to us or our management, identify
forward-looking statements. Such forward-looking statements are based on the
beliefs and assumptions of our management as well as information currently
available to us. These forward-looking statements are subject to certain risks,
uncertainties and assumptions, including but not limited to the following:

     o        risks associated with changes in tax legislation

     o        dependence on key producers and services of key personnel

     o        dependence on persistency of existing business

     o        credit risk related to renewal revenue

     o        acquisition risks

     o        risks related to significant intangible assets

     o        dependence on certain insurance companies


                                       5
<PAGE>   6

     o        dependence on information processing systems and risk of error or
              omissions

     o        competitive factors and pricing pressures

     o        risks posed by the year 2000 date change

     o        changes in legal and regulatory requirements and general economic
              conditions

Should one or more of these risks or uncertainties materialize, or should
underlying assumptions prove incorrect, actual results may vary materially from
those anticipated, expected or projected. Such forward-looking statements
reflect our current views with respect to future events and are subject to these
and other risks, uncertainties and assumptions relating to the operations,
results of operations, growth strategy and liquidity. All subsequent written and
oral forward-looking statements attributable to us or individuals acting on our
behalf are expressly qualified in their entirety by this paragraph.



                                       6
<PAGE>   7


                                   SIGNATURES

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.

                                  CLARK/BARDES HOLDINGS, INC.


                                  By:  /s/ MELVIN G. TODD
                                       -----------------------------------------
Date 8/20/99                           Melvin G. Todd, President and Chief
                                       Executive Officer


                                  By:  /s/ THOMAS M. PYRA
                                       -----------------------------------------
Date 8/20/99                           Thomas M. Pyra, Vice President and Chief
                                       Financial Officer (Principal Financial
                                       Officer)