OMB APPROVAL -------------------------- OMB Number: 3235-0006 Expires: October 31, 2003 Estimated average burden hours per response....23.3 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, 2008 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: Piper Jaffray Companies Address: 800 Nicollet Mall Suite 800 Minneapolis, MN 55402-7020 Form 13F File Number: 28-10776 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: Tim Carter Title: Treasurer Phone: 612 303-6000 Signature, Place, and Date of Signing: Tim Carter Minneapolis, MN 11/3/08 ------------------------------------- ---------------------- --------------- [Signature] [City, State] [Date] Report Type (Check only one.): [X] 13F HOLDINGS REPORT. (Check here if all holdings of this reporting manager are reported in this report.) [ ] 13F NOTICE. (Check here if no holdings reported are in this report, and all holdings are reported by other reporting manager(s).) [ ] 13F COMBINATION REPORT. (Check here if a portion of the holdings for this reporting manager are reported in this report and a portion are reported by other reporting manager(s).) FORM 13F SUMMARY PAGE Report Summary: Number of Other Included Managers: 0 Form 13F Information Table Entry Total: 138 Form 13F Information Table Value Total: $ 83,895 (thousands) List of Other Included Managers: Provide a numbered list of the name(s) and Form 13F file number(s) of all institutional investment managers with respect to which this report is filed, other than the manager filing this report. NONE COLUMN 1 COLUMN 2 COLUMN 3 COLUMN 4 COLUMN 5 COLUMN 6 COLUMN 7 COLUMN 8 ---------------------------- ---------------- --------- -------- ------------------ ---------- -------- --------------------- Value SHRS OR SH/ PUT/ INVESTMENT OTHER NAME OF ISSUER TITLE OF CLASS CUSIP (X$1000) PRN AMT PRN CALL DISCRETION MANAGERS SOLE SHARED NONE -------------- ---------------- --------- -------- --------- --- ---- ---------- -------- --------- ------ ---- ADTRAN INC COM 00738A106 58 3,000 SH 3,000 0 0 ALNYLAM PHARMACEUTICALS INC COM 02043Q107 4 150 SH 150 0 0 AMERICAN PUBLIC EDUCATION IN COM 02913V103 2 48 SH 48 0 0 AMERICAN TOWER CORP CL A 029912201 18 500 SH 500 0 0 AMERIGROUP CORP NOTE 2.000% 5/1 03073TAB8 1,935 2,400,000 PRN 2,400,000 0 0 AMERISOURCEBERGEN CORP COM 03073E105 1,694 45,000 SH CALL 45,000 0 0 AMERISOURCEBERGEN CORP COM 03073E105 10,839 287,900 SH PUT 287,900 0 0 AMERISOURCEBERGEN CORP COM 03073E105 2,767 73,500 SH 73,500 0 0 AMGEN INC COM 031162100 296 5,000 SH CALL 5,000 0 0 AMGEN INC COM 031162100 2,371 40,000 SH PUT 40,000 0 0 AMGEN INC COM 031162100 18 300 SH 300 0 0 AMR CORP COM 001765106 518 52,700 SH PUT 52,700 0 0 ANNALY CAP MGMT INC COM 035710409 21 1,575 SH 1,575 0 0 ARENA PHARMACEUTICALS INC COM 040047102 2 400 SH 400 0 0 ARRIS GROUP INC NOTE 2.000%11/1 04269QAC4 1,784 2,500,000 PRN 2,500,000 0 0 ATLAS AIR WORLDWIDE HLDGS IN COM NEW 049164205 24 600 SH 600 0 0 ATLAS AMER INC COM 049167109 9 250 SH 250 0 0 ATS MED INC NOTE 6.000%10/1 002083AB9 2,715 3,000,000 PRN 3,000,000 0 0 AUXILIUM PHARMACEUTICALS INC COM 05334D107 6 200 SH 200 0 0 BARRETT BILL CORP COM 06846N104 3 100 SH 100 0 0 BARRETT BILL CORP NOTE 5.000% 3/1 06846NAA2 336 375,000 PRN 375,000 0 0 BAXTER INTL INC COM 071813109 88 1,335 SH 1,335 0 0 BEACON ROOFING SUPPLY INC COM 073685109 11 702 SH 702 0 0 BIOMARIN PHARMACEUTICAL INC COM 09061G101 15 575 SH 575 0 0 BLACKROCK DEFINED OPPRTY CR COM 09255Q105 10 1,000 SH 1,000 0 0 CAMECO CORP COM 13321L108 65 2,900 SH 2,900 0 0 CB RICHARD ELLIS GROUP INC CL A 12497T101 872 65,200 SH 65,200 0 0 CEPHEID COM 15670R107 981 70,900 SH 70,900 0 0 CHESAPEAKE ENERGY CORP NOTE 2.750%11/1 165167BW6 1,030 1,000,000 PRN 1,000,000 0 0 CHILDRENS PL RETAIL STORES I COM 168905107 17 500 SH 500 0 0 CHINA GRENTECH CORP LTD ADR 16938P107 10 5,800 SH 5,800 0 0 CHURCH & DWIGHT INC COM 171340102 12 200 SH 200 0 0 CIENA CORP NOTE 0.250% 5/0 171779AB7 595 1,000,000 PRN 1,000,000 0 0 COGNIZANT TECHNOLOGY SOLUTIO CL A 192446102 42 1,825 SH 1,825 0 0 COMPASS MINERALS INTL INC COM 20451N101 9 175 SH 175 0 0 CONTINENTAL AIRLS INC CL B 210795308 1,668 100,000 SH PUT 100,000 0 0 CUTERA INC COM 232109108 39 3,700 SH 3,700 0 0 CYBERONICS INC COM 23251P102 903 53,100 SH 53,100 0 0 DIODES INC COM 254543101 4 200 SH 200 0 0 DIODES INC NOTE 2.250%10/0 254543AA9 3,420 4,500,000 PRN 4,500,000 0 0 DOLAN MEDIA CO COM 25659P402 25 2,469 SH 2,469 0 0 DOLBY LABORATORIES INC COM 25659T107 880 25,000 SH 25,000 0 0 DOLLAR FINL CORP NOTE 2.875% 6/3 256664AB9 2,044 3,000,000 PRN 3,000,000 0 0 EARTHLINK INC NOTE 3.250%11/1 270321AA0 1,794 1,675,000 PRN 1,675,000 0 0 ENDURANCE SPECIALTY HLDGS LT SHS G30397106 468 15,140 SH 15,140 0 0 ENERGY CONVERSION DEVICES IN NOTE 3.000% 6/1 292659AA7 1,171 1,400,000 PRN 1,400,000 0 0 ENPRO INDS INC DBCV 3.937%10/1 29355XAB3 129 100,000 PRN 100,000 0 0 EQUITABLE RES INC COM 294549100 7 200 SH 200 0 0 GAMESTOP CORP NEW CL A 36467W109 15 425 SH 425 0 0 GAP INC DEL COM 364760108 116 6,500 SH 6,500 0 0 GENENTECH INC COM NEW 368710406 266 3,000 SH 3,000 0 0 GREATBATCH INC SDCV 2.250% 6/1 39153LAB2 2,830 3,305,000 PRN 3,305,000 0 0 GUESS INC COM 401617105 6,200 178,200 SH CALL 178,200 0 0 GUESS INC COM 401617105 7,525 216,300 SH PUT 216,300 0 0 GUESS INC COM 401617105 2,018 58,000 SH 58,000 0 0 HALLMARK FINL SVCS INC EC COM NEW 40624Q203 1 107 SH 107 0 0 HANESBRANDS INC COM 410345102 20 925 SH 925 0 0 HARMONIC INC COM 413160102 18 2,148 SH 2,148 0 0 HERSHEY CO COM 427866108 138 3,500 SH CALL 3,500 0 0 HHGREGG INC COM 42833L108 34 3,500 SH 3,500 0 0 HSBC HLDGS PLC ADR A 1/40PF A 404280604 100 5,700 SH 5,700 0 0 HUMAN GENOME SCIENCES INC COM 444903108 1 100 SH 100 0 0 HUNTSMAN CORP COM 447011107 265 21,000 SH CALL 21,000 0 0 HUNTSMAN CORP COM 447011107 1,642 130,300 SH PUT 130,300 0 0 HUNTSMAN CORP COM 447011107 1,310 104,000 SH 104,000 0 0 ICONIX BRAND GROUP INC NOTE 1.875% 6/3 451055AB3 1,493 2,000,000 PRN 2,000,000 0 0 IHS INC CL A 451734107 7 150 SH 150 0 0 INTERACTIVE DATA CORP COM 45840J107 23 900 SH 900 0 0 INVERNESS MED INNOVATIONS IN COM 46126P106 150 5,000 SH PUT 5,000 0 0 INVERNESS MED INNOVATIONS IN COM 46126P106 105 3,500 SH 3,500 0 0 ISHARES TR RUSSELL 2000 464287655 680 10,000 SH PUT 10,000 0 0 ISHARES TR RUSSELL MCP GR 464287481 57 1,325 SH 1,325 0 0 ITC HLDGS CORP COM 465685105 13 250 SH 250 0 0 J CREW GROUP INC COM 46612H402 86 3,000 SH CALL 3,000 0 0 J CREW GROUP INC COM 46612H402 171 6,000 SH 6,000 0 0 JA SOLAR HOLDINGS CO LTD NOTE 4.500% 5/1 466090AA5 254 350,000 PRN 350,000 0 0 LABORATORY CORP AMER HLDGS COM NEW 50540R409 7 100 SH 100 0 0 LIMITED BRANDS INC COM 532716107 130 7,500 SH 7,500 0 0 LOGITECH INTL S A SHS H50430232 9 375 SH 375 0 0 LUMBER LIQUIDATORS INC COM 55003Q103 63 5,000 SH 5,000 0 0 MACROVISION SOLUTIONS CORP COM 55611C108 77 5,000 SH 5,000 0 0 MAGMA DESIGN AUTOMATION COM 559181102 221 55,000 SH PUT 55,000 0 0 MAGMA DESIGN AUTOMATION COM 559181102 137 34,200 SH 34,200 0 0 MAGMA DESIGN AUTOMATION NOTE 2.000% 5/1 559181AC6 2,223 2,869,000 PRN 2,869,000 0 0 MARCHEX INC CL B 56624R108 217 21,096 SH 21,096 0 0 MASIMO CORP COM 574795100 11 300 SH 300 0 0 MEDAREX INC COM 583916101 1 100 SH 100 0 0 MERRILL LYNCH & CO INC COM 590188108 51 2,000 SH PUT 2,000 0 0 MICREL INC COM 594793101 45 5,000 SH 5,000 0 0 MONOLITHIC PWR SYS INC COM 609839105 635 36,569 SH 36,569 0 0 NANOSPHERE INC COM 63009F105 1 62 SH 62 0 0 NETEASE COM INC SPONSORED ADR 64110W102 5 200 SH 200 0 0 NETFLIX INC COM 64110L106 198 6,400 SH 6,400 0 0 NORTHWESTERN CORP COM NEW 668074305 8 300 SH 300 0 0 NPS PHARMACEUTICALS INC COM 62936P103 2 300 SH 300 0 0 NYSE EURONEXT COM 629491101 2,172 55,440 SH 55,440 0 0 O2MICRO INTERNATIONAL LTD SPONS ADR 67107W100 9 2,410 SH 2,410 0 0 OCEANEERING INTL INC COM 675232102 7 125 SH 125 0 0 ODYSSEY HEALTHCARE INC COM 67611V101 711 70,000 SH CALL 70,000 0 0 OIL STS INTL INC COM 678026105 10 275 SH 275 0 0 OSI PHARMACEUTICALS INC NOTE 2.000%12/1 671040AF0 429 250,000 PRN 250,000 0 0 OSIRIS THERAPEUTICS INC COM 68827R108 2 100 SH 100 0 0 OXFORD INDS INC COM 691497309 744 28,800 SH 28,800 0 0 PENN VA CORP NOTE 4.500%11/1 707882AA4 161 140,000 PRN 140,000 0 0 PETROCHINA CO LTD SPONSORED ADR 71646E100 616 6,000 SH 6,000 0 0 PFIZER INC COM 717081103 129 7,000 SH CALL 7,000 0 0 PHARMERICA CORP COM 71714F104 2,501 111,200 SH CALL 111,200 0 0 QUANEX BUILDING PRODUCTS COR COM 747619104 6 400 SH 400 0 0 QUESTCOR PHARMACEUTICALS INC COM 74835Y101 1 100 SH 100 0 0 QUIKSILVER INC COM 74838C106 13 2,200 SH 2,200 0 0 RANGE RES CORP COM 75281A109 429 10,000 SH CALL 10,000 0 0 RANGE RES CORP COM 75281A109 429 10,000 SH PUT 10,000 0 0 RED HAT INC COM 756577102 301 20,000 SH PUT 20,000 0 0 RED HAT INC COM 756577102 226 15,000 SH 15,000 0 0 RED HAT INC DBCV 0.500% 1/1 756577AB8 320 330,000 PRN 330,000 0 0 ROYAL BK SCOTLAND GROUP PLC ADR PFD SER P 780097762 38 4,500 SH 4,500 0 0 SALIX PHARMACEUTICALS INC COM 795435106 129 20,050 SH 20,050 0 0 SANGAMO BIOSCIENCES INC COM 800677106 1 100 SH 100 0 0 SELECT SECTOR SPDR TR SBI INT-FINL 81369Y605 219 11,000 SH CALL 11,000 0 0 SELECT SECTOR SPDR TR SBI INT-FINL 81369Y605 796 40,000 SH PUT 40,000 0 0 SELECT SECTOR SPDR TR SBI INT-FINL 81369Y605 298 15,000 SH 15,000 0 0 SOLERA HOLDINGS INC COM 83421A104 7 250 SH 250 0 0 STAAR SURGICAL CO COM PAR $0.01 852312305 135 30,000 SH 30,000 0 0 STARENT NETWORKS CORP COM 85528P108 28 2,168 SH 2,168 0 0 STERICYCLE INC COM 858912108 24 400 SH 400 0 0 STRATASYS INC COM 862685104 1 51 SH 51 0 0 SYBASE INC COM 871130100 9 300 SH 300 0 0 SYNTA PHARMACEUTICALS CORP COM 87162T206 1 100 SH 100 0 0 TOWER GROUP INC COM 891777104 2 100 SH 100 0 0 TRANS1 INC COM 89385X105 4 375 SH 375 0 0 ULTRA CLEAN HLDGS INC COM 90385V107 7 1,481 SH 1,481 0 0 VITAL IMAGES INC COM 92846N104 3 200 SH 200 0 0 VOLCANO CORPORATION COM 928645100 3 182 SH 182 0 0 WEST PHARMACEUTICAL SVSC INC COM 955306105 96 1,975 SH 1,975 0 0 WISCONSIN ENERGY CORP COM 976657106 4 100 SH 100 0 0 YAHOO INC COM 984332106 121 7,000 SH CALL 7,000 0 0 YINGLI GREEN ENERGY HLDG CO ADR 98584B103 27 2,457 SH 2,457 0 0 YINGLI GREEN ENERGY HLDG CO NOTE 12/1 98584BAA1 1,418 1,750,000 PRN 1,750,000 0 0