13F-HR/A 1 q30913fa.txt Q309PCM13FHRA Form 13F Form 13F COVER PAGE Report for the Calendar Year or Quarter Ended: 30-Sep-09 Check here if Amendment [ X ] ; Amendment Number: ___1_____ This Amendment (Check only one.): [ X ] is a restatement. [ ] adds new holdings entries. Institutional Investment Manger Filing this Report: Name: Perkins Capital Management, Inc. Address: 730 East Lake Street, Wayzata, Minnesota 55391 SEC File Number: 801-22888 The institutional investment manager filing this report an 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 is understood that all required items, statements, schedules, lists and tables are considered integral parts of this form. Person signing on this Report on Behalf of Reporting Manager: Name: Richard C. Perkins Title: Executive Vice President/Portfolio Manager Phone: (952) 473-8367 Signature:/s/Richard C. Perkins Place and Date of Signing: 29-Oct-09 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).) TITLE VALUE SHARES/ SH/ PUT/ INVT OTR VOTING AUTHORITY NAME OF ISSUER OF CLASS CUSIP X1000 PRN AMT PRN CALL DSCRTN MGRS SOLE SHRD NONE ABRAXAS PETE CORP COM 003830106 233 130000 SH Sole 130000 ADDVANTAGE TECH NOLOGIES GP I COM NEW 006743306 138 60000 SH Sole 60000 ADVANCED ANALO GIC TECHNOLOGI COM 00752J108 206 52000 SH Sole 50000 2000 ALLION HEALTH CARE INC COM 019615103 682 116500 SH Sole 83000 33500 ALLSCRIPT MISYS HEALTHCAR SOL COM 01988P108 265 13050 SH Sole 8100 4950 ALNYLAM PHARMA CEUTICALS INC COM 02043Q107 498 21950 SH Sole 13100 8850 ALTRIA GROUP I COM 02209S103 272 15250 SH Sole 11750 3500 AMYLIN PHARMA CEUTICALS INC COM 032346108 179 13100 SH Sole 7000 6100 APPLIANCE RECY CLING CTRS AME COM NEW 03814F205 1811 742175 SH Sole 492300 249875 ASPENBIO PHARMA INC COM 045346103 1134 555800 SH Sole 313900 241900 AT&T CORP COM 00206R102 327 12094 SH Sole 5000 7094 ATRICURE INC COM 04963C209 133 28258 SH Sole 25658 2600 ATS MED INC COM 002083103 1745 651020 SH Sole 209536 441484 BIOSCRIP INC COM 09069N108 504 74500 SH Sole 42500 32000 BLUEPHOENIX SOLUTIONS LTD SHS M20157109 2175 573952 SH Sole 196575 377377 BOEING CO COM 097023105 355 6550 SH Sole 4950 1600 BOSTON SCIEN TIFIC CORP COM 101137107 480 45350 SH Sole 26100 19250 BRIDGELINE SOFTWARE INC COM 10807Q205 25 21070 SH Sole 21070 BRISTOL MYERS SQUIBB CO COM 110122108 1093 48550 SH Sole 23200 25350 BRUSH ENGINEERED MATLS INC COM 117421107 387 15834 SH Sole 11584 4250 CARDICA INC COM 14141R101 773 512244 SH Sole 269793 242451 CARDIOVASCULAR SYS INC DEL COM 141619106 1371 188600 SH Sole 79000 109600 CBL & ASSOC PPTYS INC COM 124830100 129 13343 SH Sole 1000 12343 CLARIENT INC COM 180489106 931 221100 SH Sole 28400 192700 CLICKSOFTWARE TECHNOLOGIES L ORD M25082104 631 100250 SH Sole 40000 60250 COMPELLENT TECH NOLOGIES INC COM 20452A108 1136 62950 SH Sole 19700 43250 COMPUTER TASK GROUP INC COM 205477102 908 112000 SH Sole 104000 8000 CONCEPTUS INC COM 206016107 1087 58650 SH Sole 30850 27800 CONEXANT SYSTEMS INC COM NEW 207142308 370 135000 SH Sole 135000 CONSTELLATION BRANDS INC CL A 21036P108 542 35750 SH Sole 13650 22100 CORVEL CORP COM 221006109 1120 39450 SH Sole 19450 20000 CYTORI THERA PEUTICS INC COM 23283K105 4069 1030196 SH Sole 580024 450172 DATALINK CORP COM 237934104 1091 303040 SH Sole 82750 220290 DELUXE CORP COM 248019101 598 34950 SH Sole 22775 12175 DEXCOM INC COM 252131107 3184 401516 SH Sole 233950 167566 DIAMOND FOODS INC COM 252603105 1305 41150 SH Sole 22650 18500 DIGIRAD CORP COM 253827109 152 53500 SH Sole 53500 DONALDSON INC COM 257651109 1414 40830 SH Sole 17650 23180 DOT HILL SYS CORP COM 25848T109 747 429169 SH Sole 130776 298393 EBIX INC COM NEW 278715206 1384 25000 SH Sole 25000 EDAP TMS S A SPN ADR 268311107 200 50000 SH Sole 50000 ENDOLOGIX INC COM 29266S106 3599 581401 SH Sole 273902 307499 ENZO BIOCHEM INC COM 294100102 177 25000 SH Sole 25000 EPLUS INC COM 294268107 459 29500 SH Sole 25000 4500 EVERGREEN SOLAR INC COM 30033R108 336 175000 SH Sole 37000 138000 FSI INTL INC COM 302633102 116 100000 SH Sole 100000 FULLER H B CO COM 359694106 787 37654 SH Sole 16104 21550 GENERAL DYNAMICS CORP COM 369550108 578 8950 SH Sole 4900 4050 GLOBAL TRAFFIC NETWORK INC COM 37947B103 719 154037 SH Sole 53325 100712 GLOBECOMM SYSTEMS INC COM 37956X103 1188 163401 SH Sole 49662 113739 GRAINGER W W INC COM 384802104 608 6802 SH Sole 3402 3400 GRANITE CITY FOOD & BREWERY COM 38724Q107 156 324996 SH Sole 57000 267996 GULFMARK OFFSHORE INC COM 402629109 792 24200 SH Sole 10300 13900 HANSEN MEDICAL INC COM 411307101 481 137500 SH Sole 44000 93500 HEALTH CARE REIT INC COM 42217K106 491 11800 SH Sole 5250 6550 HEALTH FITNESS CORP COM NEW 42217V201 5950 1064316 SH Sole 495800 568516 HESKA CORP COM 42805E108 88 200000 SH Sole 200000 HOLOGIC INC COM 436440101 194 11900 SH Sole 8700 3200 HYPERCOM CORP COM 44913M105 31 10000 SH Sole 10000 ILLUMINA INC COM 452327109 3094 72800 SH Sole 44400 28400 IMAGE SENSING SYS INC COM 45244C104 674 52100 SH Sole 25900 26200 INCONTACT INC COM 45336E109 313 105000 SH Sole 46500 58500 INSIGNIA SYS INC COM 45765Y105 4944 1304610 SH Sole 944343 360267 INTEGRAMED AMER INC COM NEW 45810N302 675 71000 SH Sole 65000 6000 INTEGRATED SILICON SOL COM 45812P107 56 15000 SH Sole 15000 INTERNATIONAL BUSINESS MACHS COM 459200101 362 3026 SH Sole 1601 1425 ISIS PHARMA CEUTICALS INC COM 464330109 3598 246916 SH Sole 144400 102516 JOHNSON & JOHNSON INC COM 478160104 659 10820 SH Sole 6270 4550 LAKES ENTMNT INC COM 51206P109 297 88419 SH Sole 64000 24419 LILLY ELI & CO COM 532457108 945 28600 SH Sole 13100 15500 MAKO SURGICAL CORP COM 560879108 201 23000 SH Sole 18000 5000 MANPOWER INC COM 56418H100 795 14023 SH Sole 6173 7850 MEDTOX SCIENTIFIC INC COM 584977201 733 80500 SH Sole 25000 55500 MEDTRONIC INC COM 585055106 343 9324 SH Sole 3900 5424 MIDWAY GOLD CORP COM 598153104 54 75000 SH Sole 75000 MOLSON COORS BREWING CO CL B 60871R209 1178 24200 SH Sole 9900 14300 MULTIBAND CORP COM NEW 62544X209 92 44000 SH Sole 4000 40000 NATURAL HEALTH TRENDS CORP CMPR.001 63888P406 50 100000 SH Sole 100000 NATUS MEDICAL INC DEL COM 639050103 783 50725 SH Sole 19225 31500 NAVARRE CORP COM 639208107 2585 1175000 SH Sole 510000 665000 NETSCOUT SYS INC COM 64115T104 405 30000 SH Sole 30000 NORTECH SYS INC COM 656553104 120 43500 SH Sole 30500 13000 NOVATEL WIRELESS INC COM NEW 66987M604 199 17500 SH Sole 17500 OCULUS INNOVATIVE SCIENCES I COM 67575P108 1371 564237 SH Sole 279637 284600 ONCOTHYREON INC COM 682324108 3607 692386 SH Sole 423912 268474 OPENTV CORP CL A G67543101 68 49250 SH Sole 14000 35250 ORTHOVITA INC COM 68750U102 4731 1077661 SH Sole 527150 550511 PATTERSON COMPANIES INC COM 703395103 1290 47350 SH Sole 18750 28600 PATTERSON UTI ENERGY INC COM 703481101 1027 68000 SH Sole 32500 35500 PENTAIR INC COM 709631105 678 22967 SH Sole 12467 10500 PETROLEUM DEV CORP COM 716578109 215 11500 SH Sole 9000 2500 PFIZER INC COM 717081103 1445 87290 SH Sole 26700 60590 POLYMET MINING CORP COM 731916102 167 63500 SH Sole 63500 PRICELINE COM INC COM NEW 741503403 456 2750 SH Sole 1750 1000 PRIDE INTL INC DEL COM 74153Q102 826 27150 SH Sole 12100 15050 RAINMAKER SYSTEM COM NEW 750875304 802 557200 SH Sole 238000 319200 RAMTRON INTL CORP COM NEW 751907304 631 249362 SH Sole 105000 144362 RCM TECH NOLOGIES INC COM NEW 749360400 414 185000 SH Sole 123000 62000 REAL GOODS SOLAR INC CL A 75601N104 174 66678 SH Sole 15500 51178 REGENERX BIOPHAR MACEUTICALS COM 75886X108 51 60000 SH Sole 40000 20000 REVLON INC CL A NEW 761525609 97 20000 SH Sole 20000 ROCKWELL MEDICAL TECH COM 774374102 3430 440900 SH Sole 50000 390900 ROSETTA GENOMICS LTD SHS M82183100 278 121357 SH Sole 32000 89357 RTI BIO LOGICS INC COM 74975N105 944 217050 SH Sole 81250 135800 SAFE BULKERS INC COM Y7388L103 203 25000 SH Sole 25000 SANOFI AVENTIS SPN ADR 80105N105 244 6600 SH Sole 3000 3600 SEATTLE GENETICS INC COM 812578102 445 31700 SH Sole 21900 9800 SPAN AMER MED SYS INC COM 846396109 361 27750 SH Sole 21000 6750 ST JUDE MED INC COM 790849103 3162 81048 SH Sole 15500 65548 STAAR SURGICAL CO CMPR.01 852312305 3082 755434 SH Sole 412600 342834 SUPERVALU INC COM 868536103 2591 172050 SH Sole 89300 82750 SYNOVIS LIFE TECH NOLOGIES IN COM 87162G105 4419 320200 SH Sole 194350 125850 TARGET CORP COM 87612E106 205 4400 SH Sole 4400 TCF FINL CORP COM 872275102 1097 84100 SH Sole 37400 46700 TENNANT CO COM 880345103 1265 43520 SH Sole 23500 20020 TEREX CORP NEW COM 880779103 442 21300 SH Sole 11300 10000 TRANS1 INC COM 89385X105 257 53450 SH Sole 32450 21000 TRINITY BIOTECH PLC SPNDRNW 896438306 40 10000 SH Sole 10000 UNITEDHEALTH GROUP INC COM 91324P102 637 25450 SH Sole 9300 16150 UROLOGIX INC COM 917273104 3305 2777404 SH Sole 1615300 1162104 UROPLASTY INC COM NEW 917277204 1061 842102 SH Sole 434500 407602 U.S. AUTO PARTS NETWORK INC COM 90343C100 245 45000 SH Sole 45000 US BANCORP CORP DEL COM NEW 902973304 637 29147 SH Sole 15197 13950 U S PHYSICAL THERAPY INC COM 90337L108 1218 80850 SH Sole 48500 32350 USEC INC COM 90333E108 188 40000 SH Sole 40000 VERSO PAPER CORP COM 92531L108 598 200000 SH Sole 200000 VIRTUAL RADIOL OGIC CORPORATI COM 92826B104 819 62850 SH Sole 39000 23850 VIRTUSA CORP COM 92827P102 470 49500 SH Sole 13000 36500 VITAL IMAGES INC COM 92846N104 6280 501610 SH Sole 174603 327007 WAL MART STORES INC COM 931142103 447 9103 SH Sole 4503 4600 WIRELESS RONIN TECHNOLOGIES COM 97652A203 7328 2064354 SH Sole 835060 1229294 WPT ENTER PRISES INC COM 98211W108 145 148181 SH Sole 136477 11704 XOMA LTD ORD G9825R107 296 365500 SH Sole 281000 84500 ZIX CORP COM 98974P100 6141 2791103 SH Sole 1192653 1598450 ZOLTEK COS INC COM 98975W104 147 14000 SH Sole 12000 2000 TOTAL VALUE 146166 DATA RECORDS 135 OTHER MANAGERS ON WHOSE BEHALF REPORT IS FILED 0