13F-HR 1 q30813f.txt 3Q0813F UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Form 13F Form 13F COVER PAGE Report for the Calendar Year or Quarter Ended: 30-Sep-08 Check here if Amendment [ ] ; Amendment Number: ________ This Amendment (Check only one.): [ ] 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's 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: Wayzata, MN 30-Oct-08 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).) NAME TITLE VALUE SHRS/ SH/ PUT/ INVSTMT OTR VOTING AUTHORITY OF ISSUER OF CLASSCUSIP x$1000 PRN MAT PRN CALL DSCRTN MGRS SOLE SHRD NONE ACCENTURE LTD BERMUDA CL A G1150G111 707 18600 SH Sole 6900 11700 ADDVANTAGE TECH NOLOGIES GP I COM NEW 006743306 134 50000 SH Sole 50000 AERO GROW INTL INC COM 00768M103 168 61900 SH Sole 31250 30650 ALLION HEALTH CARE INC COM 019615103 298 50000 SH Sole 50000 ALLSCRIPTS HEALTH CARE SOLUTI COM 01988P108 256 20550 SH Sole 13700 6850 ALNYLAM PHARMA CEUTICALS INC COM 02043Q107 958 33075 SH Sole 20575 12500 AMER BIO MEDICA CORP COM 024600108 212 416500 SH Sole 345000 71500 APPLIANCE RECY CLING CTRS AME COM NEW 03814F205 3053 725275 SH Sole 477300 247975 ASPENBIO PHARMA INC COM 045346103 1586 254200 SH Sole 142900 111300 ATS MED INC COM 002083103 1724 596620 SH Sole 206120 390500 BANK OF AMERICA CORPORATION COM 060505104 217 6202 SH Sole 3900 2302 BIOSCRIP INC COM 09069N108 498 167100 SH Sole 105600 61500 BLUEPHOENIX SOLUTIONS LTD SHS M20157109 166 47225 SH Sole 13925 33300 BOSTON SCIEN TIFIC CORP COM 101137107 885 72100 SH Sole 27850 44250 BRUSH ENGINEERED MATLS INC COM 117421107 331 17850 SH Sole 11000 6850 CARDICA INC COM 14141R101 1680 206425 SH Sole 64350 142075 CBL & ASSOC PPTYS INC COM 124830100 218 10850 SH Sole 5400 5450 CLARIENT INC COM 180489106 455 258300 SH Sole 31600 226700 COMPELLENT TECH NOLOGIES INC COM 20452A108 2937 228350 SH Sole 113750 114600 COMPUTER TASK GROUP INC COM 205477102 650 100000 SH Sole 100000 CONCEPTUS INC COM 206016107 1350 81450 SH Sole 43550 37900 CONOCOPHILLIPS COM 20825C104 392 5353 SH Sole 2003 3350 CONSTELLATION BRANDS INC CL A 21036P108 655 30500 SH Sole 12650 17850 CORVEL CORP COM 221006109 1183 41350 SH Sole 18450 22900 CYTORI THERA PEUTICS INC COM 23283K105 3182 602569 SH Sole 310017 292552 DATALINK CORP COM 237934104 1256 287450 SH Sole 132750 154700 DELUXE CORP COM 248019101 185 12850 SH Sole 5175 7675 DEXCOM INC COM 252131107 2464 398100 SH Sole 234100 164000 DIAMOND FOODS INC COM 252603105 1818 64875 SH Sole 37175 27700 DIGITAL ANGEL CORP NEW COM 25383A101 8 21350 SH Sole 16800 4550 DONALDSON INC COM 257651109 1148 27400 SH Sole 9600 17800 DOT HILL SYS CORP COM 25848T109 907 403095 SH Sole 138920 264175 EASYLINK SERVICES INTL CORP CL A 277858106 165 50000 SH Sole 50000 EBIX INC COM NEW 278715206 940 10000 SH Sole 10000 EDAP TMS S A SPN ADR 268311107 117 60000 SH Sole 60000 ENDOLOGIX INC COM 29266S106 1465 704362 SH Sole 333700 370662 ENTRUST INC COM 293848107 1064 494800 SH Sole 300800 194000 EV3 INC COM 26928A200 581 57900 SH Sole 38000 19900 FULLER H B CO COM 359694106 815 39054 SH Sole 16504 22550 GENERAL MLS INC COM 370334104 207 3006 SH Sole 1406 1600 GLOBAL TRAFFIC NETWORK INC COM 37947B103 2019 217837 SH Sole 63725 154112 GLOBECOMM SYSTEMS INC COM 37956X103 2955 338065 SH Sole 126725 211340 GRAINGER W W INC COM 384802104 592 6802 SH Sole 3102 3700 GRANITE CITY FOOD & BREWERY COM 38724Q107 443 680897 SH Sole 150717 530180 HEALTH CARE REIT INC COM 42217K106 916 17200 SH Sole 8650 8550 HESKA CORPORATION COM 42805E108 130 200000 SH Sole 200000 ILLUMINA INC COM 452327109 4094 101000 SH Sole 62250 38750 IMAGE SENSING SYS INC COM 45244C104 686 59000 SH Sole 27900 31100 I-MANY INC COM 44973Q103 173 247583 SH Sole 246583 1000 INSIGNIA SYS INC COM 45765Y105 2561 1306267 SH Sole 942500 363767 INTEGRAMED AMER INC COM NEW 45810N302 465 65000 SH Sole 65000 INTERNATIONAL BUSINESS MACHS COM 459200101 354 3027 SH Sole 1602 1425 ISIS PHARMA CEUTICALS INC COM 464330109 4867 288150 SH Sole 170300 117850 ITERIS INC COM 46564T107 248 125000 SH Sole 125000 JOHNSON & JOHNSON COM 478160104 985 14220 SH Sole 7670 6550 LAKES ENTMNT INC COM 51206P109 596 90300 SH Sole 64000 26300 LANDEC CORP COM 514766104 246 30000 SH Sole 30000 LUMINEX CORP DEL COM 55027E102 575 23000 SH Sole 15250 7750 MANPOWER INC COM 56418H100 639 14800 SH Sole 6150 8650 MATHSTAR INC COM NEW 576801302 176 163353 SH Sole 55687 107666 MATRIXX INI TATIVES INC COM 57685L105 447 25000 SH Sole 25000 MEDTOX SCIEN TIFIC INC COM NEW 584977201 717 58082 SH Sole 58082 MEDTRONIC INC COM 585055106 809 16150 SH Sole 3600 12550 MIDWAY GOLD CORP COM 598153104 81 75000 SH Sole 75000 MONOGRAM BIO SCIENCES INC COM 60975U108 786 1034550 SH Sole 323550 711000 MULTIBAND CORP COM NEW 62544X209 70 44000 SH Sole 4000 40000 NATURAL HEALTH TRENDS CORP CPR.001 63888P406 52 100000 SH Sole 100000 NATURE VISION INC COM 63902E106 75 106495 SH Sole 43605 62890 NAVARRE CORP COM 639208107 29 20000 SH Sole 20000 NETSCOUT SYS INC COM 64115T104 239 22500 SH Sole 22500 NORTECH SYS INC COM 656553104 189 37500 SH Sole 29500 8000 OCULUS INNOVATIVE SCIENCES I COM 67575P108 843 443387 SH Sole 193317 250070 ON2 TECH NOLOGIES INC COM 68338A107 538 1536100 SH Sole 465475 1070625 ONCOTHYREON INC COM 682324108 762 645899 SH Sole 390862 255037 OPENTV CORP CL A G67543101 208 147550 SH Sole 93550 54000 ORTHOVITA INC COM 68750U102 3104 1193750 SH Sole 588950 604800 PATTERSON COMPANIES INC COM 703395103 462 15200 SH Sole 3000 12200 PENTAIR INC COM 709631105 562 16257 SH Sole 9207 7050 PFIZER INC COM 717081103 1462 79272 SH Sole 21382 57890 POKERTEK INC COM 730864105 56 18150 SH Sole 18150 POLYMET MINING CORP COM 731916102 144 65250 SH Sole 65250 PRIDE INTL INC DEL COM 74153Q102 780 26350 SH Sole 10300 16050 RAINMAKER SYSTEMS COM NEW 750875304 396 176000 SH Sole 63000 113000 RAMTRON INTL CORP COM NEW 751907304 714 259697 SH Sole 110697 149000 RCM TECH NOLOGIES INC COM NEW 749360400 298 171337 SH Sole 105000 66337 REAL GOODS SOLAR INC CL A 75601N104 277 67000 SH Sole 16500 50500 RIMAGE CORP COM 766721104 901 64515 SH Sole 15750 48765 ROCKWELL MEDICAL TECH COM 774374102 1830 442200 SH Sole 50000 392200 ROSETTA GENOMICS LTD SHS M82183100 354 135000 SH Sole 35500 99500 SEATTLE GENETICS INC COM 812578102 2046 191250 SH Sole 110250 81000 SECURE COM PUTING CORP COM 813705100 411 75000 SH Sole 75000 SOFTBRANDS INC COM 83402A107 1470 1528461 SH Sole 695350 833111 SPAN AMER MED SYS INC COM 846396109 360 30250 SH Sole 23500 6750 SPARTAN MTRS INC COM 846819100 149 46775 SH Sole 40250 6525 SPECTRUM BRANDS INC COM 84762L105 91 65500 SH Sole 63500 2000 ST JUDE MED INC COM 790849103 3577 82248 SH Sole 15500 66748 STAAR SURGICAL CO CMPR.01 852312305 1994 444200 SH Sole 260400 183800 STEN CORP COM 85857T101 95 100000 SH Sole 100000 SUMTOTAL SYS INC COM 866615107 1081 264236 SH Sole 90180 174056 SUPERVALU INC COM 868536103 302 13900 SH Sole 3200 10700 SURMODICS INC COM 868873100 240 7625 SH Sole 4525 3100 SYNOVIS LIFE TECH NOLOGIES IN COM 87162G105 6304 334950 SH Sole 188350 146600 SYNTA PHARMA CEUTICALS CORP COM 87162T206 179 23500 SH Sole 19500 4000 TARGET CORP COM 87612E106 235 4800 SH Sole 4800 TCF FINL CORP COM 872275102 1316 73090 SH Sole 25840 47250 TENNANT CO COM 880345103 1594 46520 SH Sole 25500 21020 TRINITY BIOTECH PLC SPNADRN 896438306 926 328400 SH Sole 121400 207000 UNITEDHEALTH GROUP INC COM 91324P102 716 28200 SH Sole 9800 18400 UROLOGIX INC COM 917273104 2109 1741675 SH Sole 980875 760800 UROPLASTY INC COM NEW 917277204 2113 880602 SH Sole 449500 431102 US BANCORP DEL COM NEW 902973304 1037 28784 SH Sole 13834 14950 U S PHYSICAL THERAPY INC COM 90337L108 1404 80850 SH Sole 48500 32350 VITAL IMAGES INC COM 92846N104 8037 535784 SH Sole 168120 367664 VOLCANO CORPORATION COM 928645100 255 14750 SH Sole 5250 9500 WAL MART STORES INC COM 931142103 545 9103 SH Sole 4503 4600 WESTMORE LAND COAL CO COM 960878106 186 11800 SH Sole 3500 8300 WIRELESS RONIN TECHNOLOGIES COM 97652A203 2782 1169183 SH Sole 421395 747788 WYETH COM 983024100 548 14832 SH Sole 5938 8894 XOMA LTD ORD G9825R107 591 281500 SH Sole 217500 64000 ZIX CORP COM 98974P100 5908 2614301 SH Sole 972350 1641951 TOTAL VALUE 126541 DATA RECORDS 120 OTHER MANAGERS ON WHOSE BEHALF REPORT IS FILED 0