13F-HR 1 q40613f.txt FOURTH QUARTER 2006 13F UNITED STATES SECURITIES AND EXCHANGE COMMISSION "Washington, D.C. 20549" Form 13F Form 13F COVER PAGE Report for the Calendar Year or Quarter Ended: 31-Dec-2006 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 24-Jan-2007 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 CLSS CUSIP (x$1000) PRN MAT PRN CALL DSCRTN MGRS SOLE SHRD NONE ABBOTT LABS COM 002824100 223 4575 SH Sole 300 4275 ACE LTD COM G0070K103 781 12900 SH Sole 3900 9000 ADEZA BIO MEDICAL CORP COM 006864102 593 39750 SH Sole 22850 16900 AFFYMETRIX INC COM 00826T108 493 21400 SH Sole 9350 12050 AGILENT TECH NOLOGIES INC COM 00846U101 387 11100 SH Sole 5100 6000 ALLIANCE IMAGING INC COM NEW 018606202 850 127750 SH Sole 51000 76750 AMERICAN DENTAL PARTNERS COM 025353103 236 12500 SH Sole 12500 AMERICAN EXPRESS CO COM 025816109 270 4450 SH Sole 1675 2775 AMERICAN SHARED HOSPITAL SVC COM 029595105 200 30000 SH Sole 30000 AMERICAN TECHNOLOGY CORP COM NEW 030145205 196 50000 SH Sole 50000 AMYLIN PHARMA CEUTICALS INC COM 032346108 1259 34900 SH Sole 18850 16050 APPLIANCE RE CYCLING CTRS AME COM NEW 03814F205 1712 796250 SH Sole 680850 115400 APPLIX INC COM 038316105 312 27500 SH Sole 27500 ARCHSTONE SMITH TR COM 039583109 253 4350 SH Sole 1825 2525 ART TECHNOLOGY GROUP INC COM 04289L107 37 16000 SH Sole 7000 9000 ASYST TECHNOLOGY CORP COM 04648X107 183 25000 SH Sole 25000 AVNET INC COM 053807103 386 15100 SH Sole 5500 9600 BAKER HUGHES INC COM 057224107 302 4050 SH Sole 1500 2550 BANK OF AMERICA CORPORATION COM 060505104 683 12802 SH Sole 6075 6727 BIO IMAGING TECHNOLOGIES INC COM 09056N103 419 52000 SH Sole 50000 2000 BIOMIRA INC COM 09161R106 2403 2107500 SH Sole 1061100 1046400 BOSTON SCIENTIFIC CORP COM 101137107 966 56250 SH Sole 15500 40750 CAPTARIS INC COM 14071N104 235 30300 SH Sole 11000 19300 CARDICA INC COM 14141R101 91 19250 SH Sole 5250 14000 CARDIOTECH INTL INC COM 14160C100 98 50000 SH Sole 50000 CBL & ASSOC PPTYS INC COM 124830100 1125 25950 SH Sole 9650 16300 CHARMING SHOPPES INC COM 161133103 697 51550 SH Sole 17000 34550 CHOLESTECH CORP COM 170393102 1004 54500 SH Sole 30000 24500 CIPRICO INC COM 172529109 1110 183549 SH Sole 64750 118799 COMPUTER SCIENCES CORP COM 205363104 209 3920 SH Sole 600 3320 CONCEPTUS INC COM 206016107 2650 124450 SH Sole 63950 60500 CONOCOPHILLIPS COM 20825C104 378 5250 SH Sole 1850 3400 CORVEL CORP COM 221006109 2021 42475 SH Sole 22000 20475 COST-U-LESS INC COM 221492101 419 52000 SH Sole 52000 CRITICARE SYS INC COM 226901106 940 312210 SH Sole 91250 220960 DELPHAX TECHNOLOGIES INC COM 24712X106 299 242848 SH Sole 195000 47848 DELUXE CORP COM 248019101 1269 50375 SH Sole 17100 33275 DIGITAL ANGEL CORP COM 253830103 64 25250 SH Sole 13000 12250 DONALDSON INC COM 257651109 996 28700 SH Sole 5000 23700 DOT HILL SYS CORP COM 25848T109 1832 466100 SH Sole 87200 378900 DOVER CORP COM 260003108 267 5450 SH Sole 2900 2550 DYAX CORP COM 26746E103 340 112100 SH Sole 60600 51500 DYNEGY INC NEW CL A 26816Q101 1030 142300 SH Sole 34000 108300 EBIX INC COM NEW 278715206 454 16250 SH Sole 16250 ELECTRONICS FOR IMAGING INC COM 286082102 292 11000 SH Sole 3500 7500 ENCYSIVE PHARMA CEUTICALS INC COM 29256X107 398 94600 SH Sole 50350 44250 ENDOLOGIX INC COM 29266S106 2759 788417 SH Sole 302700 485717 ENTRUST INC COM 293848107 1884 441270 SH Sole 106970 334300 EON COMMU NICATION CORP COM 268763109 186 129350 SH Sole 31000 98350 EXPLORATION CO COM NEW 302133202 567 42500 SH Sole 6500 36000 FORTUNE INDUSTRIES INC COM NEW 34963X200 184 35000 SH Sole 35000 FULLER H B CO COM 359694106 705 27290 SH Sole 8250 19040 GENERAL ELECTRIC CO COM 369604103 513 13800 SH Sole 11500 2300 GLIMCHER RLTY TR SH BEN INT 379302102 421 15750 SH Sole 7050 8700 GLOBAL TRAFFIC NETWORK INC COM 37947B103 826 160750 SH Sole 27250 133500 GLOBECOMM SYSTEMS INC COM 37956X103 3335 378585 SH Sole 92500 286085 GRAINGER W W INC COM 384802104 241 3450 SH Sole 1750 1700 GRANITE CITY FOOD & BREWERY COM 38724Q107 3893 760433 SH Sole 396797 363636 HEALTH CARE REIT INC COM 42217K106 1152 26775 SH Sole 10225 16550 HEI INC COM 404160103 696 451817 SH Sole 155500 296317 HERSHEY CO COM 427866108 239 4800 SH Sole 4800 HESKA CORP COM 42805E108 210 125000 SH Sole 125000 ILLUMINA INC COM 452327109 4031 102550 SH Sole 50475 52075 I-MANY INC COM 44973Q103 209 126500 SH Sole 125000 1500 ING GROEP NV SPON ADR 456837103 953 21580 SH Sole 6500 15080 INNOVEX INC COM 457647105 313 179700 SH Sole 105700 74000 INSIGNIA SYS INC COM 45765Y105 3647 1195717 SH Sole 990200 205517 INTEGRAMED AMER INC COM NEW 45810N302 602 40000 SH Sole 40000 ISIS PHARMA CEUTICALS INC COM 464330109 6964 626260 SH Sole 247375 378885 I-TRAX INC COM NEW 45069D203 7043 2271780 SH Sole 803700 1468080 JOHNSON & JOHNSON INC COM 478160104 591 8950 SH Sole 3775 5175 KMG CHEMICALS INC COM 482564101 1127 112650 SH Sole 49250 63400 KYPHON INC COM 501577100 456 11280 SH Sole 6330 4950 LAKES ENTMNT INC COM 51206P109 256 23700 SH Sole 23700 LANDEC CORP COM 514766104 215 20000 SH Sole 20000 LEVEL 3 COMMU NICATIONS INC COM 52729N100 2052 366500 SH Sole 127900 238600 LIFECELL CORP COM 531927101 1957 81075 SH Sole 40300 40775 LIFECORE BIOMEDICAL INC COM 532187101 5576 312725 SH Sole 186475 126250 LINSAY CORPORATION COM 535555106 661 20250 SH Sole 6600 13650 MANPOWER INC COM 56418H100 772 10300 SH Sole 2050 8250 MARATHON OIL CORP COM 565849106 370 4000 SH Sole 1700 2300 MATHSTAR INC COM 576801203 2005 462956 SH Sole 154154 308802 MATRITECH INC COM 576818108 97 144700 SH Sole 16500 128200 MATRIXX INITIATIVES INC COM 57685L105 199 12500 SH Sole 12500 MCMORAN EXPLORATION CO COM 582411104 373 26250 SH Sole 18000 8250 MEDTOX SCIENTIFIC INC COM NEW 584977201 5335 400193 SH Sole 257678 142515 MEDTRONIC INC COM 585055106 1393 26035 SH Sole 4500 21535 MEDWAVE INC COM 585081102 64 110440 SH Sole 79688 30752 MERCK & CO INC COM 589331107 384 8800 SH Sole 8400 400 MICROTUNE INC DEL COM 59514P109 1441 306612 SH Sole 58200 248412 MICRUS ENDO VASCULAR CORP COM 59518V102 2141 112225 SH Sole 43775 68450 MONOGRAM BIOSCIENCES INC COM 60975U108 1980 1112540 SH Sole 239000 873540 MOSAIC CO COM 61945A107 660 30900 SH Sole 12000 18900 NATIONAL CITY CORP COM 635405103 216 5900 SH Sole 5000 900 NATIONAL TECH NICAL SYS INC COM 638104109 239 35000 SH Sole 35000 NATURE VISION INC COM 63902E106 347 60690 SH Sole 33500 27190 NBTY INC COM 628782104 717 17250 SH Sole 5600 11650 NORTECH SYS INC COM 656553104 146 19000 SH Sole 18000 1000 NORTHFIELD LABS INC COM 666135108 550 135200 SH Sole 65650 69550 OPENTV CORP CL A G67543101 1369 589875 SH Sole 121550 468325 ORTHOVITA INC COM 68750U102 1478 407100 SH Sole 201000 206100 PATTERSON COMPANIES INC COM 703395103 504 14200 SH Sole 2000 12200 PEMSTAR INC COM 706552106 3489 906250 SH Sole 380700 525550 PENTAIR INC COM 709631105 467 14880 SH Sole 5100 9780 PETROLEUM DEV CORP COM 716578109 581 13500 SH Sole 3000 10500 PFIZER INC COM 717081103 1822 70329 SH Sole 13700 56629 POKERTEK INC COM 730864105 701 84675 SH Sole 8000 76675 POLYMET MINING CORP COM 731916102 2336 744100 SH Sole 362000 382100 POWERWAVE TECH NOLOGIES INC COM 739363109 810 125650 SH Sole 48850 76800 PRIDE INTL INC DEL COM 74153Q102 447 14880 SH Sole 5000 9880 PW EAGLE INC COM 69366Y108 844 24440 SH Sole 24440 QUOVADX INC COM 74913K106 84 29800 SH Sole 11750 18050 RCM TECH NOLOGIES INC COM NEW 749360400 78 13000 SH Sole 2500 10500 REGIS CORP MINN COM 758932107 1728 43700 SH Sole 8750 34950 RIMAGE CORP COM 766721104 2032 78164 SH Sole 13950 64214 RITA MED SYS INC DEL COM 76774E103 439 95500 SH Sole 40500 55000 ROCHESTER MED CORP COM 771497104 603 50000 SH Sole 50000 ROCKWELL MEDICAL TECH COM 774374102 3245 455200 SH Sole 160000 295200 RUSH ENTER PRISES INC CL A 781846209 494 29200 SH Sole 20000 9200 SCHOOL SPECIALTY INC COM 807863105 820 21880 SH Sole 5500 16380 SECURE COMPUTING CORP COM 813705100 88 13350 SH Sole 2500 10850 SOCKET COMMUNI CATION INC COM 833672108 494 440973 SH Sole 87373 353600 SONIC INNO VATIONS INC COM 83545M109 261 50000 SH Sole 50000 SPAN AMER MED SYS INC COM 846396109 251 17171 SH Sole 16421 750 SPARTAN MTRS INC COM 846819100 411 27100 SH Sole 21500 5600 SPECTRA NETICS CORP COM 84760C107 557 49300 SH Sole 7000 42300 ST JUDE MED INC COM 790849103 3994 109248 SH Sole 8000 101248 SUMTOTAL SYS INC COM 866615107 715 118206 SH Sole 52312 65894 SUPERCONDUCTOR TECHNOLOGIES COM NEW 867931305 171 96500 SH Sole 55000 41500 SUPERVALU INC COM 868536103 601 16800 SH Sole 4000 12800 SURMODICS INC COM 868873100 615 19750 SH Sole 10125 9625 SYMANTEC CORP COM 871503108 269 12900 SH Sole 2600 10300 SYNOVIS LIFE TECHNOLOGIES IN COM 87162G105 3365 338150 SH Sole 218500 119650 TARGET CORP COM 87612E106 342 6000 SH Sole 6000 TCF FINL CORP COM 872275102 1065 38850 SH Sole 4000 34850 TENNANT CO COM 880345103 1035 35680 SH Sole 10350 25330 TEXAS INSTRS INC COM 882508104 337 11695 SH Sole 650 11045 THIRD WAVE TECHNOLOGIES INC COM 88428W108 2049 426000 SH Sole 203450 222550 TITAN PHARMA CEUTICALS INC DE COM 888314101 133 40000 SH Sole 29500 10500 TVIA INC COM 87307P101 401 355000 SH Sole 95000 260000 UROLOGIX INC COM 917273104 1275 542650 SH Sole 262950 279700 UROPLASTY INC COM NEW 917277204 1493 606602 SH Sole 412102 194500 US BANCORP DEL COM NEW 902973304 1264 34921 SH Sole 13884 21037 VITAL IMAGES INC COM 92846N104 17606 505925 SH Sole 183850 322075 VIVUS INC COM 928551100 192 53000 SH Sole 50000 3000 WELLS FARGO & CO NEW COM 949746101 364 10250 SH Sole 3300 6950 WIRELESS RONIN TECHNOLOGIES COM 97652A203 4806 834355 SH Sole 283191 551164 WPT ENTER PRISES INC COM 98211W108 118 30600 SH Sole 30000 600 WYETH COM 983024100 473 9294 SH Sole 2550 6744 ZIX CORP COM 98974P100 3127 2628000 SH Sole 774300 1853700 TOTAL VALUE 177498 DATA RECORDS 150 OTHER MANAGERS ON WHOSE BEHALF REPORT IS FILED 0