13F-HR 1 3Q2012.txt Form 13F Form 13F COVER PAGE Report for the Calendar Year or Quarter Ended: 30-September-2012 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, 11/08/2012 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).) TTL OF VALUE SHARES/ SH/ PUT/ INV OTR VOTING AUTHORITY NAME OF ISSUER CLASS CUSIP (x1000) PRN AMT PRN CALL DISC MGRS SOLE SHRD NONE ABBOTT LABS COM 002824100 1472 21475 SH Sole 14525 6950 ACTUATE CORP COM 00508B102 2008 285700 SH Sole 214000 71700 AEGION CORP COM 00770F104 885 46200 SH Sole 31100 15100 AFLAC INC COM 001055102 785 16400 SH Sole 11350 5050 ALPHATEC HOLDINGS INC COM 02081G102 744 450650 SH Sole 399900 50750 ALTRIA GROUP INC COM 02209S103 426 12750 SH Sole 12250 500 AMERICAN WTR WKS CO INC NEW COM 030420103 541 14600 SH Sole 10300 4300 APPLIANCE RECY CLING CTRS AME COM NEW 03814F205 2814 849978 SH Sole 611978 238000 ARABIAN AMERN DEV CO COM 038465100 269 27500 SH Sole 26000 1500 ASPENBIO PHARMA INC CMPR001 045346301 2021 729583 SH Sole 598412 131171 AT&T INC COM 00206R102 298 7912 SH Sole 5912 2000 BACTERIN INTL HLDGS INC COM 05644R101 954 615500 SH Sole 552000 63500 BAXTER INTL INC COM 071813109 1446 23990 SH Sole 17340 6650 BEMIS INC COM 081437105 223 7100 SH Sole 5750 1350 BLACK DIAMOND INC COM 09202G101 175 20000 SH Sole 20000 BRIDGELINE DIGITAL INC COM 10807Q205 293 248700 SH Sole 228700 20000 BRISTOL MYERS SQUIBB CO COM 110122108 1672 49550 SH Sole 35550 14000 CALIX INC COM 13100M509 278 43387 SH Sole 15371 28016 CALLIDUS SOFTWARE INC COM 13123E500 599 121500 SH Sole 106250 15250 CARDICA INC COM 14141R101 1065 739532 SH Sole 652062 87470 CARDIOME PHARMA CORP COM NEW 14159U202 23 70000 SH Sole 70000 CARDIONET INC COM 14159L103 1366 541868 SH Sole 490618 51250 CARDIOVASCULAR SYS INC DEL COM 141619106 3463 299600 SH Sole 175550 124050 CHEVRON CORP NEW COM 166764100 680 5836 SH Sole 4376 1460 COLEMAN CABLE INC COM 193459302 1187 123100 SH Sole 91750 31350 COMPUTER TASK GROUP INC COM 205477102 2001 123700 SH Sole 109300 14400 COVIDIEN PLC SHS G2554F113 389 6550 SH Sole 4850 1700 CRYOLIFE INC COM 228903100 148 22000 SH Sole 22000 CVS CAREMARK CORPORATION COM 126650100 821 16950 SH Sole 12900 4050 CYTORI THERA PEUTICS INC COM 23283K105 2949 668600 SH Sole 459000 209600 DATALINK CORP COM 237934104 1679 202750 SH Sole 138250 64500 DELUXE CORP COM 248019101 1049 34325 SH Sole 26925 7400 DEXCOM INC COM 252131107 440 29300 SH Sole 17600 11700 DIGIRAD CORP COM 253827109 1082 522616 SH Sole 474166 48450 DONALDSON INC COM 257651109 1034 29800 SH Sole 15800 14000 DOT HILL SYS CORP COM 25848T109 1096 1024705 SH Sole 862205 162500 EBIX INC COM NEW 278715206 944 40000 SH Sole 40000 ECHO GLOBAL LOGISTICS INC COM 27875T101 837 48800 SH Sole 37300 11500 ECOTALITY INC COM NEW 27922Y202 76 165000 SH Sole 137250 27750 EDAP TMS S A SPN ADR 268311107 1652 966000 SH Sole 764000 202000 ELECTROMED INC COM 285409108 397 273800 SH Sole 245800 28000 EMERALD OIL INC COM 29101U100 1018 1226393 SH Sole 1108040 118353 ENDOCYTE INC COM 29269A102 120 12000 SH Sole 10500 1500 ENDOLOGIX INC COM 29266S106 1667 120600 SH Sole 79700 40900 EPLUS INC COM 294268107 1745 44500 SH Sole 40000 4500 EXACT SCIENCES CORP COM 30063P105 820 74500 SH Sole 62900 11600 EXPRESS INC COM 30219E103 479 32350 SH Sole 20200 12150 FAMOUS DAVES AMER INC COM 307068106 1335 140050 SH Sole 96300 43750 GENERAL MLS INC COM 370334104 213 5356 SH Sole 3356 2000 GLAXOSMITH KLINE PLC SPN ADR 37733W105 763 16500 SH Sole 11350 5150 GLOBECOMM SYSTEMS INC COM 37956X103 1283 115103 SH Sole 103103 12000 GLU MOBILE INC COM 379890106 1072 230950 SH Sole 207700 23250 GRANITE CITY FOOD & BREWERY COM NEW 38724Q404 94 41999 SH Sole 333 41666 GSV CAP CORP COM 36191J101 987 114350 SH Sole 72250 42100 HANSEN MEDICAL INC COM 411307101 3500 1803950 SH Sole 1390650 413300 HEALTH CARE REIT INC COM 42217K106 426 7375 SH Sole 4275 3100 INCONTACT INC COM 45336E109 1981 304775 SH Sole 280525 24250 INFUSYSTEM HLDGS INC COM 45685K102 1575 894859 SH Sole 783859 111000 INNER WORKINGS INC COM 45773Y105 1544 118600 SH Sole 88000 30600 INSIGNIA SYS INC COM 45765Y105 469 272867 SH Sole 111000 161867 INTERNATIONAL BUSINESS MACHS COM 459200101 841 4055 SH Sole 2625 1430 INVENTURE FOODS INC COM 461212102 1359 238905 SH Sole 167500 71405 ISIS PHARMA CEUTICALS INC COM 464330109 1484 105464 SH Sole 77264 28200 JOHNSON & JOHNSON COM 478160104 575 8340 SH Sole 5190 3150 JONES SODA CO COM 48023P106 453 1562500 SH Sole 1328500 234000 LAKES ENTMNT INC COM 51206P109 128 60100 SH Sole 53150 6950 LEMAITRE VASCULAR INC COM 525558201 459 71508 SH Sole 61208 10300 LIFE VANTAGE CORP COM 53222K106 2949 859672 SH Sole 107425 752247 LILLY ELI & CO COM 532457108 1344 28350 SH Sole 19500 8850 MEDTRONIC INC COM 585055106 714 16550 SH Sole 10850 5700 METROPOLITAN HLTH NETWORKS COM 592142103 560 60000 SH Sole 60000 MGC DIAG NOSTICS CORP COM 552768103 307 51000 SH Sole 51000 MICROSOFT CORP COM 594918104 1051 35325 SH Sole 24175 11150 MIDWAY GOLD CORP COM 598153104 131 80000 SH Sole 18750 61250 MULTIBAND CORP COM NEW 62544X209 606 282000 SH Sole 207000 75000 NANOSPHERE INC COM 63009F105 1055 317750 SH Sole 292750 25000 NAVARRE CORP COM 639208107 1869 1190664 SH Sole 469000 721664 NCR CORP NEW COM 62886E108 1134 48650 SH Sole 33200 15450 NETSCOUT SYS INC COM 64115T104 765 30000 SH Sole 30000 NEUROMETRIX INC COM NEW 641255203 118 193000 SH Sole 163000 30000 NORTECH SYS INC COM 656553104 133 37000 SH Sole 33500 3500 NOVADAQ TECH NOLOGIES INC COM 66987G102 2784 269250 SH Sole 228500 40750 OCULUS INNOVATIVE SCIENCES I COM 67575P108 70 74000 SH Sole 52000 22000 ONCOTHYREON INC COM 682324108 3031 590851 SH Sole 410301 180550 ORION ENERGY SYSTEMS INC COM 686275108 1237 624645 SH Sole 557445 67200 PENTAIR LTD COM 709631105 840 18875 SH Sole 13025 5850 PFIZER INC COM 717081103 1858 74776 SH Sole 42131 32645 PHARMATHENE INC COM 71714G102 1310 1110100 SH Sole 779800 330300 PLANAR SYS INC COM 726900103 23 17314 SH Sole 17314 POLYMET MINING CORP COM 731916102 81 69500 SH Sole 13750 55750 RAINMAKER SYSTEMS COM NEW 750875304 2668 2242285 SH Sole 1999785 242500 RENTECH INC COM 760112102 41 16485 SH Sole 16485 RESEARCH FRONTIERS INC COM 760911107 966 217000 SH Sole 203000 14000 RIMAGE CORP COM 766721104 695 103000 SH Sole 70500 32500 ROCKWELL MED INC COM 774374102 3503 428750 SH Sole 58250 370500 ROYAL DUTCH SHELL PLC SPNADRB 780259107 510 7150 SH Sole 5000 2150 RTI BIOLOGICS INC COM 74975N105 2098 502000 SH Sole 441700 60300 SANOFI SPN ADR 80105N105 924 21450 SH Sole 16500 4950 SCHOOL SPECIALTY INC COM 807863105 446 194000 SH Sole 187500 6500 SCRIPPS E W CO OHIO CLANEW 811054402 213 20000 SH Sole 20000 SEQUENOM INC COM NEW 817337405 464 131500 SH Sole 109500 22000 SMUCKER J M CO COM NEW 832696405 827 9575 SH Sole 7475 2100 SOLTA MED INC COM 83438K103 1209 385000 SH Sole 350000 35000 SPS COMM INC COM 78463M107 1920 49900 SH Sole 33750 16150 ST JUDE MED INC COM 790849103 3225 76538 SH Sole 26050 50488 STAAR SURGICAL CO CMPR.01 852312305 2432 321650 SH Sole 216850 104800 SUPERCONDUCTOR TECHNOLOGIES COM NEW 867931305 78 165762 SH Sole 163762 2000 SUPERVALU INC COM 868536103 1123 466050 SH Sole 262550 203500 SYNERGETICS USA INC COM 87160G107 1047 212000 SH Sole 158000 54000 SYNERGY RES CORP COM 87164P103 354 85000 SH Sole 85000 TARGET CORP COM 87612E106 244 3850 SH Sole 3450 400 TRANS1 INC COM 89385X105 2697 1021693 SH Sole 789703 231990 U S PHYSICAL THERAPY INC COM 90337L108 2418 87500 SH Sole 67650 19850 U.S. AUTO PARTS NETWORK INC COM 90343C100 494 142800 SH Sole 79800 63000 UNI PIXEL INC COM NEW 904572203 511 82500 SH Sole 81250 1250 UNITEDHEALTH GROUP INC COM 91324P102 1252 22600 SH Sole 14950 7650 UQM TECH NOLOGIES INC COM 903213106 68 58750 SH Sole 48250 10500 UROLOGIX INC COM 917273104 4386 5770621 SH Sole 4185902 1584719 UROPLASTY INC COM NEW 917277204 4507 1182881 SH Sole 738033 444848 US BANCORP DEL COM NEW 902973304 772 22510 SH Sole 16640 5870 VERIZON COMMUNI CATIONS INC COM 92343V104 332 7296 SH Sole 7296 WIRELESS RONIN TECHNOLOGIES COM 97652A203 3706 3944873 SH Sole 3231255 713618 XILINX INC COM 983919101 324 9705 SH Sole 9705 ZIX CORP COM 98974P100 2544 889642 SH Sole 690442 199200 TOTAL VALUE 141639 DATA RECORDS 124 OTHER MANAGERS ON WHOSE BEHALF REPORT 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