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

                                   FORM 13F

                             FORM 13F COVER PAGE

REPORT FOR THE CALENDAR YEAR OR QUARTER ENDED:  9/30/06

CHECK HERE IF AMENDMENT ( ); AMENDMENT NUMBER:
THIS AMENDMENT (CHECK ONLY ONE.):  ( ) RESTATEMENT.
                                   ( ) ADDS NEW HOLDINGS ENTRIES.

INSTITUTIONAL INVESTMENT MANAGER FILING THIS REPORT:

NAME:        COMMERCE BANCSHARES, INC.
ADDRESS:     1000 WALNUT, P.O. BOX 13686
             KANSAS CITY, MO 64199

FORM 13F FILE NUMBER:  28-642

THE INSTITUTIONAL INVESTMENT MANAGER FILING THIS REPORT AND THE
PERSON BY WHOM IT IS SIGNED HEREBY REPRESENT THAT THE PERSON
SIGNING THE REPORT IS AUTHORIZED TO SUBMIT IT, THAT ALL
INFORMATION CONTAINED HEREIN IS TRUE, CORRECT AND COMPLETE, AND
THAT IT IS UNDERSTOOD THAT ALL REQUIRED ITEMS, STATEMENTS
SCHEDULES, LISTS, AND TABLES, ARE CONSIDERED INTEGRAL PARTS OF
THIS FORM.

PERSON SIGNING THIS REPORT ON BEHALF OF REPORTING MANAGER:

NAME:         JEFFERY D. ABERDEEN
TITLE:        CONTROLLER
PHONE:        816-234-2081

SIGNATURE, PLACE, AND DATE OF SIGNING:

JEFFERY D. ABERDEEN         KANSAS CITY, MO       10/1/06

REPORT TYPE (CHECK ONLY ONE.):

( )           13F HOLDINGS REPORT

( )           13F NOTICE

(X)           13F COMBINATION REPORT

LIST OF OTHER MANAGERS REPORTING FOR THIS MANAGER:
28-05260      COMMERCE BANK, N.A. (MISSOURI)
28-04263      COMMERCE BANK, N.A. (WICHITA, KS)

I AM SIGNING THIS REPORT AS REQUIRED BY THE SECURITIES EXCHANGE ACT
OF 1934.


                                 FORM 13F SUMMARY PAGE

REPORT SUMMARY:

NUMBER OF OTHER INCLUDED MANAGERS:             0

FORM 13F INFORMATION TABLE ENTRY TOTAL:        10

FORM 13F INFORMATION TABLE VALUE TOTAL:      $37,025
                                           (THOUSANDS)

LIST OF OTHER INCLUDED MANAGERS:
   NONE




FORM 13F INFORMATION TABLE
                                          
                                                          VALUE     SHARES/  SH/  PUT/  INVSTMT   OTHER       VOTING AUTHORITY
NAME OF ISSUER               TITLE OF CLASS     CUSIP    (X1000)    PRN AMT  PRN  CALL  DSCRETN  MANAGERS    SOLE  SHARED  NONE
--------------------------   --------------     -----    -------    -------  ---  ----  -------  --------    ----  ------  ----
BANK OF AMERICA CORPORATION  COMMON STOCK     060505104     6114     114132   SH        SOLE               114132
BRISTOL MYERS SQUIBB CO.     COMMON STOCK     110122108     1468      58922   SH        SOLE                58922
EDWARDS, A.G.                COMMON STOCK     281760108     1332      25000   SH        SOLE                25000
GOLDMAN SACHS                COMMON STOCK     38141G104      338       2000   SH        SOLE                 2000
JOHNSON AND JOHNSON          COMMON STOCK     478160104     2173      33461   SH        SOLE                33461
J.P. MORGAN CHASE & CO.      COMMON STOCK     616880100     3502      74575   SH        SOLE                74575
SUNTRUST BANKS, INC.         COMMON STOCK     867914103     5255      68000   SH        SOLE                68000
US BANCORP                   COMMON STOCK     917292104     5516     166055   SH        SOLE               166055
WACHOVIA CORPORATION 2ND NEW COMMON STOCK     929903102     5480      98200   SH        SOLE                98200
WELLS FARGO & CO. NEW        COMMON STOCK     949746101     5847     161600   SH        SOLE               161600