13F-HR 1 q10913f.txt Form 13F Form 13F COVER PAGE Report for the Calendar Year or Quarter Ended: 31-Mar-09 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 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: "Wayzata, MN" 27-Apr-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).) VOTING AUTHORITY TITLE VALUE SHARES/ SH/ PUT/ INVT OTR NAME OF ISSUER OF CLASS CUSIP X1000 PRN AMT PRN CALL DSCRTN MGRS SOLE SHRD NONE ATS MED INC COM 002083103 1334 533520 SH Sole 169036 364484 ADDVANTAGE TECH NOLOGIES GP INC COM NEW 006743306 71 50000 SH Sole 50000 ALLION HEALTH CARE INC COM 019615103 288 62500 SH Sole 51000 11500 AMER BIO MEDICA CORP COM 024600108 58 416500 SH Sole 345000 71500 AMYLIN PHARMA CEUTICALS INC COM 032346108 152 12950 SH Sole 8000 4950 ASPENBIO PHARMA INC COM 045346103 596 358800 SH Sole 214400 144400 BOSTON SCIEN TIFIC CORP COM 101137107 361 45350 SH Sole 26100 19250 BRISTOL MYERS SQUIBB CO COM 110122108 1119 51050 SH Sole 22700 28350 BRUSH ENGINEERED MATLS INC COM 117421107 218 15750 SH Sole 11500 4250 CARDIOVASCULAR SYS INC DEL COM 141619106 480 67687 SH Sole 2987 64700 CLARIENT INC COM 180489106 509 226100 SH Sole 28400 197700 COMPUTER TASK GROUP INC COM 205477102 276 80000 SH Sole 80000 CONCEPTUS INC COM 206016107 832 70850 SH Sole 35850 35000 CORVEL CORP COM 221006109 802 39650 SH Sole 19450 20200 DATALINK CORP COM 237934104 1103 381740 SH Sole 132750 248990 DELUXE CORP COM 248019101 192 19950 SH Sole 12275 7675 DEXCOM INC COM 252131107 1807 436500 SH Sole 250800 185700 DIAMOND FOODS INC COM 252603105 1191 42650 SH Sole 24150 18500 DIGIRAD CORP COM 253827109 54 50000 SH Sole 50000 DONALDSON INC COM 257651109 1150 42830 SH Sole 19650 23180 EDAP TMS S A COM 268311107 90 60000 SH Sole 60000 EASYLINK SERVICES INTL CORP CL A 277858106 125 70000 SH Sole 70000 EBIX INC COM NEW 278715206 621 25000 SH Sole 25000 ENTRUST INC COM 293848107 778 515000 SH Sole 299000 216000 FULLER H B CO COM 359694106 508 39054 SH Sole 17504 21550 GRAINGER W W INC COM 384802104 477 6802 SH Sole 3402 3400 ILLUMINA INC COM 452327109 3433 92175 SH Sole 56625 35550 INTERNATIONAL BUSINESS MACHS COM 459200101 313 3226 SH Sole 1801 1425 ISIS PHARMA CEUTICALS INC COM 464330109 4022 267950 SH Sole 154950 113000 JOHNSON & JOHNSON COM 478160104 678 12895 SH Sole 7045 5850 KANA SOFTWARE INC COM 483600300 141 204687 SH Sole 59000 145687 LANDEC CORP COM 514766104 167 30000 SH Sole 30000 LILLY ELI & CO COM 532457108 956 28600 SH Sole 13100 15500 MATHSTAR INC COM 576801302 119 143659 SH Sole 53587 90072 MEDTOX SCIEN TIFIC INC COM NEW 584977201 370 55500 SH Sole 55500 MEDTRONIC INC COM 585055106 429 14574 SH Sole 2750 11824 MIDWAY GOLD CORP COM 598153104 35 75000 SH Sole 75000 NATUS MEDICAL INC DEL COM 639050103 266 31225 SH Sole 17225 14000 NAVARRE CORP COM 639208107 520 1181000 SH Sole 510000 671000 NORTECH SYS INC COM 656553104 147 42500 SH Sole 29500 13000 ONCOTHYREON INC COM 682324108 1309 692699 SH Sole 427201 265498 OSHKOSH CORP COM 688239201 203 30156 SH Sole 14656 15500 PATTERSON COMPANIES INC COM 703395103 902 47850 SH Sole 18750 29100 PATTERSON UTI ENERGY INC COM 703481101 654 73000 SH Sole 37500 35500 PENTAIR INC COM 709631105 492 22707 SH Sole 12207 10500 PFIZER INC COM 717081103 1159 85122 SH Sole 27032 58090 POKERTEK INC COM 730864105 87 86750 SH Sole 86750 POLYMET MINING CORP COM 731916102 58 73500 SH Sole 73500 PRICELINE COM INC COM NEW 741503403 217 2750 SH Sole 1750 1000 RCM TECH NOLOGIES INC COM NEW 749360400 176 170837 SH Sole 120500 50337 RAINMAKER SYSTEM COM NEW 750875304 335 549200 SH Sole 238000 311200 RAMTRON INTL CORP COM NEW 751907304 259 261362 SH Sole 105000 156362 RIMAGE CORP COM 766721104 778 58294 SH Sole 13800 44494 ROCKWELL MEDICAL TECH COM 774374102 1877 441600 SH Sole 50000 391600 ST JUDE MED INC COM 790849103 2988 82248 SH Sole 15500 66748 SEATTLE GENETICS INC COM 812578102 1377 139650 SH Sole 75200 64450 SPAN AMER MED SYS INC COM 846396109 238 27750 SH Sole 21000 6750 STAAR SURGICAL CO COM PR.01 852312305 583 583300 SH Sole 319000 264300 SUMTOTAL SYS INC COM 866615107 419 248018 SH Sole 84062 163956 SUPERCONDUCTOR TECHNOLOGIES COM NEW 867931305 10 10000 SH Sole 10000 SUPERVALU INC COM 868536103 1435 100500 SH Sole 49400 51100 TCF FINL CORP COM 872275102 1186 100840 SH Sole 52340 48500 TENNANT CO COM 880345103 436 46520 SH Sole 26500 20020 TEREX CORP NEW COM 880779103 197 21300 SH Sole 11300 10000 TRINITY BIOTECH PLC SPNADRNEW 896438306 17 10000 SH Sole 10000 US BANCORP DEL COM NEW 902973304 418 28634 SH Sole 14684 13950 UROLOGIX INC COM 917273104 899 2360825 SH Sole 1363975 996850 UROPLASTY INC COM NEW 917277204 642 867102 SH Sole 459500 407602 WAL MART STORES INC COM 931142103 474 9103 SH Sole 4503 4600 WYETH COM 983024100 638 14832 SH Sole 6938 7894 NATURE VISION INC COM 63902E106 30 106495 SH Sole 43605 62890 HESKA CORP COM 42805E108 49 200000 SH Sole 200000 AERO GROW INTL INC COM 00768M103 10 50525 SH Sole 30625 19900 ALLSCRIPT MISYS HEALTHCAR SOL COM 01988P108 191 18550 SH Sole 12700 5850 ALNYLAM PHARMA CEUTICALS INC COM 02043Q107 522 27400 SH Sole 16100 11300 APPLIANCE RECY CLING CTRS AME COM NEW 03814F205 1387 737775 SH Sole 489800 247975 BIOSCRIP INC COM 09069N108 683 292000 SH Sole 158500 133500 CARDICA INC COM 14141R101 493 169316 SH Sole 54725 114591 COMPELLENT TECHNOLOGIES INC COM 20452A108 971 89450 SH Sole 44700 44750 CONOCOPHILLIPS COM 20825C104 474 12103 SH Sole 6753 5350 CONSTELLATION BRANDS INC CL A 21036P108 427 35850 SH Sole 13650 22200 CYTORI THERA PEUTICS INC COM 23283K105 1533 891172 SH Sole 494274 396898 DOT HILL SYS CORP COM 25848T109 216 372269 SH Sole 126876 245393 ENDOLOGIX INC COM 29266S106 1181 556907 SH Sole 242902 314005 GLOBAL TRAFFIC NETWORK INC COM 37947B103 601 198209 SH Sole 63726 134483 GLOBECOMM SYSTEMS INC COM 37956X103 1636 282495 SH Sole 90177 192318 GRANITE CITY FOOD & BREWERY COM 38724Q107 127 537804 SH Sole 115450 422354 HEALTH CARE REIT INC COM 42217K106 425 13900 SH Sole 6200 7700 HEALTH FITNESS CORP COM NEW 42217V201 2594 1206511 SH Sole 556053 650458 I-MANY INC COM 44973Q103 61 243583 SH Sole 243583 IMAGE SENSING SYS INC COM 45244C104 464 52100 SH Sole 25900 26200 INSIGNIA SYS INC COM 45765Y105 2604 1301767 SH Sole 942500 359267 INTEGRAMED AMER INC COM NEW 45810N302 396 65000 SH Sole 65000 INTEGRATED SILICON SOLUTION COM 45812P107 23 15000 SH Sole 15000 ITERIS INC COM 46564T107 164 125000 SH Sole 125000 LAKES ENTMNT INC COM 51206P109 189 88419 SH Sole 64000 24419 MANPOWER INC COM 56418H100 441 14000 SH Sole 6150 7850 MATRIXX INITATIVES INC COM 57685L105 328 20000 SH Sole 20000 MOLSON COORS BREWING CO CL B 60871R209 811 23650 SH Sole 9350 14300 MONOGRAM BIO SCIENCES INC COM NEW 60975U207 351 138022 SH Sole 38879 99143 MULTIBAND CORP COM NEW 62544X209 87 44000 SH Sole 4000 40000 NATURAL HEALTH TRENDS CORP COM PR.001 63888P406 32 100000 SH Sole 100000 OCULUS INNOVATIVE SCIENCES I COM 67575P108 722 573658 SH Sole 277729 295929 ON2 TECH NOLOGIES INC COM 68338A107 371 1261412 SH Sole 353627 907785 ORTHOVITA INC COM 68750U102 2983 1113112 SH Sole 530401 582711 PRIDE INTL INC DEL COM 74153Q102 474 26350 SH Sole 11300 15050 REAL GOODS SOLAR INC CL A 75601N104 130 64678 SH Sole 15500 49178 REGENERX BIO PHARMACEUTICALS COM 75886X108 26 50000 SH Sole 35000 15000 SOFTBRANDS INC COM 83402A107 434 1606845 SH Sole 793852 812993 SYNOVIS LIFE TECHNOLOGIES IN COM 87162G105 4459 322200 SH Sole 194350 127850 SYNTA PHARMA CEUTICALS CORP COM 87162T206 67 31500 SH Sole 26500 5000 US PHYSICAL THERAPY INC COM 90337L108 783 80850 SH Sole 48500 32350 UNITEDHEALTH GROUP INC COM 91324P102 524 25050 SH Sole 9300 15750 VITAL IMAGES INC COM 92846N104 5725 507960 SH Sole 172553 335407 WIRELESS RONIN TECHNOLOGIES COM 97652A203 4120 2039754 SH Sole 800660 1239094 WPT ENTER PRISES INC COM 98211W108 107 191922 SH Sole 179931 11991 ZIX CORP COM 98974P100 2694 2641269 SH Sole 1059153 1582116 ZOLTEK COS INC COM 98975W104 85 12450 SH Sole 10950 1500 OPENTV CORP CL A G67543101 71 47250 SH Sole 10000 37250 XOMA LTD ORD G9825R107 165 311400 SH Sole 244400 67000 BLUEPHOENIX SOLUTIONS LTD SHS M20157109 583 303502 SH Sole 90275 213227 CLICKSOFTWARE TECHNOLOGIES L ORD M25082104 71 19000 SH Sole 19000 ROSETTA GENOMICS LTD SHS M82183100 360 125357 SH Sole 32000 93357 TOTAL VALUE 91706 DATA RECORDS 123 OTHER MANAGERS ON WHOSE BEHALF REPORT IS FILED 0