<PAGE>   1


                     U.S. SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549
                                    FORM 10-Q

(MARK ONE)
[X]      QUARTERLY REPORT UNDER SECTION 13 OR 15 (d) OF THE SECURITIES EXCHANGE
         ACT OF 1934

FOR THE QUARTERLY PERIOD ENDED      JUNE 30, 1999
                              --------------------

[ ]      TRANSITION REPORT UNDER SECTION 13 OR 15 (d) OF THE EXCHANGE ACT FOR
         THE TRANSITION PERIOD FROM ________________ TO ________________

COMMISSION FILE NUMBER      0-26918
                      ---------------------------------------------------------

   
                          CYTOCLONAL PHARMACEUTICS INC.
              (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)
    


<TABLE>
<S>                                                              <C>
                 DELAWARE                                                        75-2402409
(STATE OR OTHER JURISDICTION OF INCORPORATION                      (I.R.S. EMPLOYER IDENTIFICATION NUMBER)
             OR ORGANIZATION)
</TABLE>


           9000 HARRY HINES BOULEVARD, SUITE 330, DALLAS, TEXAS 75235
                    (ADDRESS OF PRINCIPAL EXECUTIVE OFFICES)

                                 (214)-353-2922
              (REGISTRANT'S TELEPHONE NUMBER, INCLUDING AREA CODE)


              (FORMER NAME, FORMER ADDRESS AND FORMER FISCAL YEAR,
                         IF CHANGED SINCE LAST REPORT)

         CHECK WHETHER THE ISSUER: (1) FILED ALL REPORTS REQUIRED TO BE FILED BY
SECTION 13 OR 15(d) OF THE EXCHANGE ACT DURING THE PAST 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
    ---------------      ----------------

                      APPLICABLE ONLY TO CORPORATE ISSUERS

         STATE THE NUMBER OF SHARES OUTSTANDING OF EACH OF THE ISSUER'S CLASSES
OF COMMON EQUITY, AS OF THE LATEST PRACTICABLE DATE: 10,395,210 SHARES OF COMMON
STOCK, $.01 PAR VALUE, OUTSTANDING AS OF AUGUST 11, 1999.




<PAGE>   2


                          CYTOCLONAL PHARMACEUTICS INC.


                                TABLE OF CONTENTS


<TABLE>
<CAPTION>
                                                                                                   Page(s)
<S>                                                                                              <C>

PART I.  FINANCIAL INFORMATION


                  Item 1. --   Financial Statements:

                               Balance Sheets as of June 30, 1999 (unaudited)
                                  and December 31, 1998                                               3

                               Statements of Operations for the Three Months                          
                                  Ended June 30, 1999 and 1998 and the Six Months
                                  Ended June 30, 1999 and 1998 (unaudited)                            3                           

                               Statements of Cash Flows for the Three Months
                                  Ended June 30, 1999 and 1998 (unaudited)                            5

                               Notes to Financial Statements                                          6


                  Item 2. --   Management's Discussion and Analysis of Financial
                                  Condition and Results of Operations                                 7



PART II.  OTHER INFORMATION


                  Item 6. --   Exhibits and Reports on Form 8-K                                       8

Signatures                                                                                            8

Exhibit 11  Computation of per share earnings                                                         9

Exhibit 27  Financial Data Schedule                                                                  10
</TABLE>





<PAGE>   3


                          PART I. FINANCIAL INFORMATION


Item 1.  Financial Statements

                          CYTOCLONAL PHARMACEUTICS INC.


                                 BALANCE SHEETS


<TABLE>
<CAPTION>
                                                                  June 30,         December 31,
                                                                    1999               1998
                                                                 (unaudited)
                                                                 ------------      ------------
<S>                                                              <C>               <C>         
                                             ASSETS

Current assets:

   Cash (principally money market)                               $  4,907,000      $  6,826,000

   Prepaid expenses and other current assets                          291,000            85,000
                                                                 ------------      ------------

          Total current assets                                      5,198,000         6,911,000

Equipment, net                                                        300,000           121,000

Patent rights, less accumulated amortization of
    $597,000 and $540,000                                             837,000           710,000

Other assets                                                            4,000             4,000
                                                                 ------------      ------------

          T O T A L                                              $  6,339,000      $  7,746,000
                                                                 ============      ============

                              LIABILITIES AND STOCKHOLDERS' EQUITY

Current Liabilities:

   Accounts payable and accrued expenses                              441,000           461,000
   Deferred revenue from research and development
     collaborative contract                                            83,000            67,000

   Current portion of royalties payable                               156,000           156,000
                                                                 ------------      ------------

           Total current liabilities                                  680,000           684,000
                                                                 ------------      ------------

Royalties payable less current portion                                969,000         1,000,000
                                                                 ------------      ------------

          Total liabilities                                         1,649,000         1,684,000
                                                                 ------------      ------------

Stockholders' equity:

    Preferred stock - $.01 par value, 10,000,000 shares
     authorized; 714,641 and 746,864 shares of Series A
     convertible preferred issued and outstanding at
     June 30, 1999 and December 31, 1998, respectively
     (liquidation value $1,787,000 and $1,872,000 at
     June 30, 1999 and December 31, 1998, respectively)                 7,000             7,000

    Common Stock - $.01 par value, 30,000,000 shares
     authorized: 10,378,412 and 10,209,844 shares issued
     and outstanding at June 30, 1999 and December 31,
     1998, respectively                                               104,000           102,000

Additional paid-in capital                                         24,323,000        23,785,000

Accumulated Deficit                                               (19,744,000)      (17,832,000)
                                                                 ------------      ------------

          Total Stockholders' Equity                                4,690,000         6,062,000
                                                                 ------------      ------------

          T O T A L                                              $  6,339,000      $  7,746,000
                                                                 ============      ============
</TABLE>



                                        3


<PAGE>   4

                          CYTOCLONAL PHARMACEUTICS INC.

                             STATEMENT OF OPERATIONS
                                   (unaudited)


<TABLE>
<CAPTION>
                                                          Three Months Ended                 Six Months Ended
                                                              June 30,                           June 30,
                                                  ------------------------------      ------------------------------
                                                      1999              1998              1999              1998
                                                  ------------      ------------      ------------      ------------
<S>                                               <C>               <C>               <C>               <C>         
Revenue:
  Licensing & research collaborative
     agreement                                    $    250,000      $    789,000      $    483,000      $    789,000
                                                  ------------      ------------      ------------      ------------
Operating Expenses:
  Research and development                        $    510,000      $    462,000      $  1,382,000      $    822,000
  General and administrative                           626,000           564,000         1,139,000         1,011,000
                                                  ------------      ------------      ------------      ------------
                                                     1,136,000         1,026,000         2,521,000         1,833,000
                                                  ------------      ------------      ------------      ------------

Operating (loss)                                      (886,000)         (237,000)       (2,038,000)       (1,044,000)
                                                  ------------      ------------      ------------      ------------

Other (Income) expenses:
  Interest (income)                                    (60,000)          (68,000)         (129,000)          (87,000)

  Interest expense                                       1,000                --             3,000             2,000
                                                       (59,000)          (68,000)         (126,000)          (85,000)
                                                  ------------      ------------      ------------      ------------

NET (LOSS)                                        $   (827,000)     $   (169,000)     $ (1,912,000)     $   (959,000)

Basic and diluted
    loss per common share                         $      (0.08)     $      (0.02)     $      (0.19)     $      (0.11)

Weighted average number of
  shares outstanding - basic and
  diluted                                           10,342,000         9,727,000        10,305,000         9,286,000
</TABLE>



                                       4


<PAGE>   5

                          CYTOCLONAL PHARMACEUTICS INC.


                            STATEMENTS OF CASH FLOWS
                                   (unaudited)



<TABLE>
<CAPTION>
                                                                          Six Months Ended
                                                                             June 30,
                                                                 ------------------------------
                                                                     1999              1998
                                                                 ------------      ------------
<S>                                                              <C>               <C>          
Cash flows from operating activities:
   Net (loss)                                                    $ (1,912,000)     $   (959,000)
   Adjustments to reconcile net (loss) to net
      cash (used in) operating activities:
      Depreciation and amortization                                    80,000            62,000
      Value assigned to common shares and options                     291,000
      Changes in:
        Other assets                                                 (206,000)           (9,000)
        Deferred revenue                                               16,000           461,000
        Accounts payable and accrued expenses                         (35,000)          259,000
                                                                 ------------      ------------
          Net cash (used in) operating activities                  (1,766,000)         (186,000)
                                                                 ------------      ------------

Cash flows from investing activities:
   Purchase of equipment                                             (187,000)          (56,000)
                                                                 ------------      ------------
          Net cash (used in) investing activities                    (187,000)          (56,000)
                                                                 ============      ============

Cash flows from financing activities:
   Net Proceeds from private placement                                     --         4,838,000
   Proceeds from exercise of options and warrants                      65,000         2,617,000
   Payment of royalties                                               (31,000)          (31,000)
                                                                 ------------      ------------
            Net cash provided by financing activities                  34,000         7,424,000
                                                                 ------------      ------------
NET INCREASE (DECREASE) IN CASH                                    (1,919,000)        7,182,000
Cash at beginning of period                                         6,826,000         1,849,000
                                                                 ------------      ------------
CASH AT END OF PERIOD                                            $  4,907,000      $  9,031,000
                                                                 ============      ============
Supplemental disclosures of cash flow information:
     Noncash investing activities:
          Equipment acquired included in accounts
             payable and accrued expenses:                       $     15,000
</TABLE>




                                        5


<PAGE>   6


                          CYTOCLONAL PHARMACEUTICS INC.

                          NOTES TO FINANCIAL STATEMENTS
                                  June 30, 1999
                                   (unaudited)


(1)      FINANCIAL STATEMENT PRESENTATION

         The unaudited financial statements of Cytoclonal Pharmaceutics Inc., a
         Delaware corporation (the "Company"), included herein have been
         prepared in accordance with the rules and regulations promulgated by
         the Securities and Exchange Commission and, in the opinion of
         management, reflect all adjustments (consisting only of normal
         recurring accruals) necessary to present fairly the results of
         operations for the interim periods presented. 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.
         However, management believes that the disclosures are adequate to make
         the information presented not misleading. These financial statements
         and the notes thereto should be read in conjunction with the financial
         statements and the notes thereto included in the Company's Annual
         Report on Form 10-K for the fiscal year ended December 31, 1998. The
         results for the interim periods are not necessarily indicative of the
         results for the full fiscal year.

         Through June 1998, the Company was in the development stage and its
         efforts had been principally devoted to research and development,
         capital formation and organizational development.

(2)      RESEARCH AND COLLABORATIVE AGREEMENT

         In June 1998, the Company entered into a license and research agreement
         with Bristol-Myers Squibb ("BMS") on two technologies related to
         production of paclitaxel, the active ingredient in BMS's largest
         selling cancer product, Taxol(R). The agreement includes fees,
         milestone payments, research and development support and minimum and
         sales based royalties.

(3)      LOSS PER COMMON SHARE

         In 1997, the Financial Accounting Standards Board issued Statement No.
         128 "Earnings Per Share". Statement No. 128 replaced the calculation of
         primary and fully diluted earnings per share with basic and diluted
         earnings per share. Unlike primary earnings per share, basic earnings
         per share excludes any dilutive effects of option, warrants and
         convertible securities. Dilutive earnings per share is very similar to
         the previously reported fully diluted earnings per share. In accordance
         with Statement No. 128, which was adopted by the Company in 1997, basic
         and diluted net loss per common share is based on the net loss
         increased by dividends on preferred stock divided by the weighted
         average number of common shares outstanding during the year. No effect
         has been given to outstanding options, warrants or convertible
         preferred stock in the diluted computation as their effect would be
         antidilutive.

 (4)     REVENUE RECOGNITION

         Revenue from licensing and research agreements is recognized as the
         expenses for research and development activities performed under the
         terms of the agreements are incurred. Revenues from nonrefundable
         licenses and up front fees are recognized upon signing the agreement.
         Revenue resulting from the achievement of milestones is recognized when
         the milestone is achieved. Amounts received in advance of services to
         be performed are recorded as deferred revenue.


                                       6


<PAGE>   7




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

         The following discussion should be read in conjunction with, and is
qualified in its entirety by, the Financial Statements and the Notes thereto
included in this report. This discussion contains certain forward-looking
statements that involve substantial risks and uncertainties. When used in this
report, the words "anticipate," "believe," "estimate," "expect" and similar
expressions as they relate to the Company or its management are intended to
identify such forward-looking statements. The Company's actual results,
performance or achievements could differ materially from those expressed in, or
implied by, these forward-looking statements. Historical operating results are
not necessarily indicative of the trends in operating results for any further
period.

         Cytoclonal Pharmaceutics Inc., a Delaware corporation (the "Company"),
was duly organized and commenced operations in September 1991. To date, the
Company's efforts have been principally devoted to research and development
activities and organizational efforts, including the development of products for
the treatment of cancer and infectious diseases, recruiting its scientific and
management personnel and advisors and raising capital.

         For the period from April 1, 1999 to June 30, 1999, the Company
incurred a net loss of $827,000 compared to a net loss of $169,000 for the same
period in 1998. For the period from January 1, 1999 to June 30, 1999, the
Company incurred a net loss of $1,912,000 compared to a net loss of $959,000 for
the same period in 1998. The increase for the six-month period from the previous
year was attributable to an increase in operating expenses and a decrease in
revenue, partially offset by an increase in interest income. The Company expects
to incur additional losses in the foreseeable future.

         The Company incurred general and administrative expenses of $1,139,000
and $1,011,000 for the six months ended June 1999 and June 1998, respectively.
The increase from the previous year was attributable to increased expenditures
for travel and lodging, consulting fees, rent, administrative salaries and
taxes, partially offset by a decrease in legal and professional expenses due to 
certain reimbursements of such costs from licensor.

         The Company incurred research and development expenses of $1,382,000
and $822,000 for the six months ended June 1999 and June 1998, respectively. The
increase was attributable to a large extent to a non-recurring expense for the
acquisition of the Quantum Core Technology(TM) for drug design and for research
activities in Israel. Additionally, the increase was attributable to funding for
the research program at Research & Development Institute, Inc. (RDI), an
increase in laboratory rental expenses, an increase in contract labor costs, an
increase in laboratory supplies, and an increase in research salaries and
payroll taxes, partially offset by a decrease in the expense for the research
program at Washington State University. Included in research and development
expenses for the six months ended June 1999 was a non-cash charge of $291,000
relating to the valuations of common stock and options issued in connection with
services rendered in identifying and securing the drug design technology.

         The Company believes that it has sufficient capital to finance the
Company's plan of operation in excess of 12 months. However, there can be no
assurances that the Company will generate sufficient revenues, if any, to fund
its operations after such period or that any required financings will be
available, through bank borrowings, debt or equity offerings, or otherwise, on
acceptable terms or at all.


                                       7


<PAGE>   8


 
                          PART II. OTHER INFORMATION



Item 6.   EXHIBITS AND REPORTS ON FORM 8-K

          (a)      Exhibit 11 Computation of net (loss) per share
                   Exhibit 27 Financial Data Schedule

          (b)      Reports on Form 8-K - None







                                   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.



                                         CYTOCLONAL PHARMACEUTICS INC.



Date: August 16, 1999                    /s/ Daniel M. Shusterman
                                         ------------------------------
                                         Daniel M. Shusterman
                                         Vice President of Operations,
                                         Treasurer and Chief Financial
                                         Officer


                                       8


<PAGE>   9



                               INDEX TO EXHIBITS


<TABLE>
<CAPTION>
Exhibit
Number              Description
-------             -----------
<S>           <C>
  11           Computation of net (loss) per share

  27           Financial Data Schedule
</TABLE>










<PAGE>   1
                                                                      EXHIBIT 11

                          CYTOCLONAL PHARMACEUTICS INC.


                   COMPUTATION OF NET (LOSS) PER COMMON SHARE
                                   (unaudited)



<TABLE>
<CAPTION>
                                                                         THREE MONTHS                          SIX MONTHS
                                                                         ENDED JUNE 30,                      ENDED JUNE 30,
                                                                 ------------------------------      ------------------------------
                                                                     1999              1998              1999              1998
                                                                 ------------      ------------      ------------      ------------
<S>                                                              <C>               <C>               <C>               <C>          
Net (loss)                                                       $   (827,000)     $   (169,000)     $ (1,912,000)     $   (959,000)

Add cumulative preferred dividend                                     (45,000)          (51,000)          (89,000)         (103,000)
                                                                 ------------      ------------      ------------      ------------

NET (LOSS) USED FOR COMPUTATION                                  $   (872,000)     $   (220,000)     $ (2,001,000)     $ (1,062,000)

Weighted average number of common shares 
  outstanding--basic and diluted                                   10,342,000         9,727,000        10,305,000         9,286,000
                                                                                                     ------------      ------------

Net (loss) per common share--basic and                         
diluted                                                          $      (0.08)     $      (0.02)     $      (0.19)     $      (0.11)
</TABLE>





                                       9







<TABLE> <S> <C>

<ARTICLE> 5
<MULTIPLIER> 1,000
       
<S>                             <C>
<PERIOD-TYPE>                   6-MOS
<FISCAL-YEAR-END>                          DEC-31-1999
<PERIOD-START>                             JAN-01-1999
<PERIOD-END>                               JUN-30-1999
<CASH>                                           4,907
<SECURITIES>                                         0
<RECEIVABLES>                                        0
<ALLOWANCES>                                         0
<INVENTORY>                                          0
<CURRENT-ASSETS>                                 5,198
<PP&E>                                             595
<DEPRECIATION>                                     295
<TOTAL-ASSETS>                                   6,339
<CURRENT-LIABILITIES>                              680
<BONDS>                                              0
<PREFERRED-MANDATORY>                                0
<PREFERRED>                                          7
<COMMON>                                           104
<OTHER-SE>                                       4,579
<TOTAL-LIABILITY-AND-EQUITY>                     6,339
<SALES>                                              0
<TOTAL-REVENUES>                                   483
<CGS>                                                0
<TOTAL-COSTS>                                        0
<OTHER-EXPENSES>                                 2,521
<LOSS-PROVISION>                                     0
<INTEREST-EXPENSE>                                   3
<INCOME-PRETAX>                                      0
<INCOME-TAX>                                         0
<INCOME-CONTINUING>                                  0
<DISCONTINUED>                                       0
<EXTRAORDINARY>                                      0
<CHANGES>                                            0
<NET-INCOME>                                   (1,912)
<EPS-BASIC>                                      (.19)
<EPS-DILUTED>                                    (.19)
        

</TABLE>