UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 13F FORM 13F COVER PAGE Report for the Calendar Year or Quarter Ended: September 30, 2006 Check here if Amendment [ ]; Amendment Number: This Amendment (Check only one.): [ ] is a restatement. [ ] adds new holdings entries. Institutional Investment Manager Filing this Report: Name:GENERAL AMERICAN INVESTORS COMPANY, INC. 13F File No. 28-461 Address: 450 Lexington Ave, Suite 3300 New York, NY 10017 13F File Number: 28-461 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: Eugene S. Stark Title: Vice-President, Administration Phone: 212-916-8447 Signature, Place, and Date of Signing: Eugene S. Stark New York, NY October 20, 2006 Report Type (Check only one.): [X] 13F HOLDINGS REPORT. [ ] 13F NOTICE. [ ] 13F COMBINATION REPORT. List of Other Managers Reporting for this Manager: Form 13F File Number Name 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: 57 Form 13F Information Table Value Total: $1241775239 List of Other Included Managers: No. 13F File Number Name COLUMN 1 COLUMN 2 COLUMN 3 COLUMN 4 COLUMN 5 COLUMN 6 COLUMN 7 COLUMN 8 --------------- ---------- ---------- --------- ---------- --------- ------- ----------- VALUE SHARES/ SH/ PUT/ INVSTMT OTHER -----VOTING AUTHORITY----- NAME OF ISSUER -TITLE OF CLASS- --CUSIP-- x$1000 PRN AMT PRN CALL DSCRETN -MANAGERS- SOLE SHARED NONE ABB Ltd. ADR COMMON 000375204 15157 1150000 SH SOLE 1150000 0 0 Arch Capital Group Ltd. COMMON G0450A105 22222 350000 SH SOLE 350000 0 0 Adams Express Company COMMON 006212104 1421 105075 SH SOLE 105075 0 0 American International Group,Inc COMMON 026874107 24848 375000 SH SOLE 375000 0 0 Alkermes, Inc. COMMON 01642T108 3804 240000 SH SOLE 240000 0 0 The Allstate Corporation COMMON 020002101 17251 275000 SH SOLE 275000 0 0 Ameriprise Financial, Inc. COMMON 03076C106 2814 60000 SH SOLE 60000 0 0 American Tower Corporation COMMON 029912201 28288 775000 SH SOLE 775000 0 0 Apache Corporation COMMON 037411105 52140 825000 SH SOLE 825000 0 0 Activision, Inc. COMMON 004930202 9438 625000 SH SOLE 625000 0 0 Avaya Inc. COMMON 053499109 6006 525000 SH SOLE 525000 0 0 AXIS Capital Holdings Limited COMMON G0692U109 13876 400000 SH SOLE 400000 0 0 Bank of America Corporation COMMON 060505104 14464 270000 SH SOLE 270000 0 0 Bed Bath & Beyond Inc. COMMON 075896100 7652 200000 SH SOLE 200000 0 0 Biogen Idec Inc. COMMON 09062X103 7596 170000 SH SOLE 170000 0 0 Berkshire Hathaway Inc. Class A COMMON 084670108 28740 300 SH SOLE 300 0 0 Cephalon, Inc. COMMON 156708109 9263 150000 SH SOLE 150000 0 0 Central Securities Corporation COMMON 155123102 675 26055 SH SOLE 26055 0 0 Costco Wholesale Corporation COMMON 22160K105 34776 700000 SH SOLE 700000 0 0 Cisco Systems, Inc. COMMON 17275R102 20682 900000 SH SOLE 900000 0 0 CEMEX, S.A. de C.V. ADR COMMON 151290889 70714 2350862 SH SOLE 2350862 0 0 Cytokinetics, Incorporated COMMON 23282W100 3890 604900 SH SOLE 604900 0 0 Diageo plc ADR COMMON 25243Q205 24864 350000 SH SOLE 350000 0 0 Dollar General Corporation COMMON 256669102 21794 1599000 SH SOLE 1599000 0 0 Genentech, Inc. COMMON 368710406 16540 200000 SH SOLE 200000 0 0 EMC Corporation COMMON 268648102 3594 300000 SH SOLE 300000 0 0 Golden West Financial COMMON 381317106 45191 585000 SH SOLE 585000 0 0 Halliburton Company COMMON 406216101 24183 850000 SH SOLE 850000 0 0 The Home Depot, Inc. COMMON 437076102 56944 1570000 SH SOLE 1570000 0 0 Intermec, Inc. COMMON 458786100 2109 80000 SH SOLE 80000 0 0 Lamar Advertising Company COMMON 512815101 18694 350000 SH SOLE 350000 0 0 Medtronic, Inc. COMMON 585055106 20898 450000 SH SOLE 450000 0 0 MedImmune, Inc. COMMON 584699102 11123 380000 SH SOLE 380000 0 0 MetLife, Inc. COMMON 59156R108 16154 285000 SH SOLE 285000 0 0 MFA Mortgage Investments, Inc. COMMON 55272X102 8009 1075000 SH SOLE 1075000 0 0 Molex Incorporated Class A COMMON 608554200 18101 550000 SH SOLE 550000 0 0 Microsoft Corporation COMMON 594918104 21880 800000 SH SOLE 800000 0 0 M&T Bank Corporation COMMON 55261F104 37188 310000 SH SOLE 310000 0 0 Annaly Capital Management, Inc. COMMON 035710409 8607 655000 SH SOLE 655000 0 0 PepsiCo, Inc. COMMON 713448108 11421 175000 SH SOLE 175000 0 0 Pfizer Inc COMMON 717081103 49261 1737000 SH SOLE 1737000 0 0 PartnerRe Ltd. COMMON G6852T105 22636 335000 SH SOLE 335000 0 0 Patterson-UTI Energy, Inc. COMMON 703481101 23760 1000000 SH SOLE 1000000 0 0 Everest Re Group, Ltd. COMMON G3223R108 52179 535000 SH SOLE 535000 0 0 Republic Services, Inc. COMMON 760759100 47247 1175000 SH SOLE 1175000 0 0 Rio Tinto plc ADR COMMON 767204100 12326 65000 SH SOLE 65000 0 0 Royce Value Trust COMMON 780910105 2458 120258 SH SOLE 120258 0 0 SunTrust Banks, Inc. COMMON 867914103 13138 170000 SH SOLE 170000 0 0 Constellation Brands, Inc. COMMON 21036P108 9354 325000 SH SOLE 325000 0 0 THQ Inc. COMMON 872443403 6272 215000 SH SOLE 215000 0 0 The TJX Companies, Inc. COMMON 872540109 65590 2340000 SH SOLE 2340000 0 0 Talisman Energy Inc. COMMON 87425E103 49140 3000000 SH SOLE 3000000 0 0 Transatlantic Holdings, Inc. COMMON 893521104 13894 230000 SH SOLE 230000 0 0 VeriSign, Inc. COMMON 92343E102 2697 133500 SH SOLE 133500 0 0 Weatherford International Ltd. COMMON G95089101 50898 1220000 SH SOLE 1220000 0 0 Wal-Mart Stores, Inc. COMMON 931142103 28359 575000 SH SOLE 575000 0 0 Xerox Corporation COMMON 984121103 29564 1900000 SH SOLE 1900000 0 0