Form 13F

Form 13F COVER PAGE

Report for the Calendar Year or Quarter Ended:	30-Sep-11

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 and 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 11-15-2011

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 OF		VALUE	SHARES/	SH/	PUT/	INV	OTR	VOTING AUTHORITY
NAME OF ISSUER	CLASS	CUSIP		(x$1000)PRN AMT	PRN	CALL	DISC	MGRS	SOLE	SHRD	NONE
ABBOTT LABS	COM	002824100	919	17975	SH		Sole		11600		6375
ACCURAY INC	COM	004397105	743	185375	SH		Sole		126650		58725
ACTUATE CORP	COM	00508B102	1620	293500	SH		Sole		211500		82000
ALPHATEC
 HOLDINGS INC	COM	02081G102	1102	522150	SH		Sole		357850		164300
ALTRIA
 GROUP INC	COM	02209S103	355	13250	SH		Sole		12250		1000
AMERICAN WTR
 WKS CO INC NEW	COM	030420103	423	14000	SH		Sole		9700		4300
ANGEION CORP	COM	03462H404	137	30000	SH		Sole		30000
APPLIANCE RECY
 CLING CTRS AME	COM NEW	03814F205	3842	857500	SH		Sole		592500		265000
ARRAY
 BIOPHARMA INC	COM	04269X105	623	319250	SH		Sole		206500		112750
ASPENBIO
 PHARMA INC	COM NEW	045346202	1952	650766	SH		Sole		385940		264826
AT&T INC	COM	00206R102	294	10312	SH		Sole		7312		3000
ATRICURE INC	COM	04963C209	2551	261950	SH		Sole		170600		91350
AUTHENTEC INC	COM	052660107	82	25000	SH		Sole				25000
AVI
 BIOPHARMA INC	COM	002346104	1794	1602000	SH		Sole		1081000		521000
BAXTER INTL INC	COM	071813109	336	5990	SH		Sole		4490		1500
BEMIS INC	COM	081437105	1197	40850	SH		Sole		28100		12750
BIOSCRIP INC	COM	09069N108	664	104375	SH		Sole		72550		31825
BRIDGELINE
 DIGITAL INC	COM	10807Q205	32	61000	SH		Sole				61000
BRISTOL MYERS
 SQUIBB CO	COM	110122108	1476	47050	SH		Sole		30350		16700
CALIX INC	COM	13100M509	207	26496	SH		Sole		5371		21125
CARDICA INC	COM	14141R101	1078	555652	SH		Sole		400524		155128
CARDIOME
 PHARMA CORP	COM NEW	14159U202	230	70000	SH		Sole		70000
CARDIONET INC	COM	14159L103	958	319200	SH		Sole		219300		99900
CARDIOVASCULAR
 SYS INC DEL	COM	141619106	4752	417220	SH		Sole		244180		173040
COLEMAN
 CABLE INC	COM	193459302	381	45000	SH		Sole		45000
COMPUTER TASK
 GROUP INC	COM	205477102	1262	113000	SH		Sole		100000		13000
CONCEPTUS INC	COM	206016107	276	26400	SH		Sole		14200		12200
CVS CAREMARK
 CORPORATION	COM	126650100	247	7350	SH		Sole		4050		3300
CYBEROPTICS
    CORP	COM	232517102	111	14000	SH		Sole		12500		1500
CYTORI THERA
 PEUTICS INC	COM	23283K105	1705	577850	SH		Sole		364550		213300
DATALINK CORP	COM	237934104	1321	194290	SH		Sole		91290		103000
DELUXE CORP	COM	248019101	673	36200	SH		Sole		25750		10450
DEXCOM INC	COM	252131107	1820	151700	SH		Sole		98900		52800
DIAMOND
 FOODS INC	COM	252603105	399	5000	SH		Sole		5000
DIGIRAD CORP	COM	253827109	899	406830	SH		Sole		248630		158200
DONALDSON INC	COM	257651109	1992	36350	SH		Sole		21950		14400
DOT HILL
 SYS CORP	COM	25848T109	1889	1250690	SH		Sole		813730		436960
DYNAMICS
 RESH CORP	COM	268057106	370	41500	SH		Sole		33000		8500
EBIX INC	COM NEW	278715206	882	60000	SH		Sole		60000
ECHO GLOBAL
 LOGISTICS INC	COM	27875T101	692	52000	SH		Sole		35000		17000
ECOTALITY INC	COM NEW	27922Y202	350	188000	SH		Sole		99000		89000
EDAP TMS S A 	COM	268311107	70	40000	SH		Sole		40000
ELECTROMED INC	COM	285409108	350	100000	SH		Sole		75000		25000
EMCORE CORP	COM	290846104	51	52000	SH		Sole		50000		2000
ENDOCYTE INC	COM	29269A102	189	17800	SH		Sole		6300		11500
ENDOLOGIX INC	COM	29266S106	3957	394119	SH		Sole		224669		169450
EPLUS INC	COM	294268107	1098	44500	SH		Sole		36500		8000
EXACT
 SCIENCES CORP	COM	30063P105	684	103100	SH		Sole		71300		31800
FAMOUS DAVES
 AMER INC	COM	307068106	1246	145050	SH		Sole		90300		54750
FSI INTL INC	COM	302633102	41	22000	SH		Sole		17000		5000
GENERAL
 MLS INC	COM	370334104	231	6012	SH		Sole		3212		2800
GENUINE
 PARTS CO	COM	372460105	390	7675	SH		Sole		6675		1000
GLAXOSMITH
 KLINE PLC	SPN ADR	37733W105	462	11200	SH		Sole		6850		4350
GLOBECOMM
 SYSTEMS INC	COM	37956X103	1687	124903	SH		Sole		70073		54830
GRAINGER
 W W INC	COM	384802104	890	5952	SH		Sole		3802		2150
GRANITE CITY
 FOOD & BREWERY	COM NEW	38724Q404	97	42082	SH		Sole		333		41749
HANSEN
 MEDICAL INC	COM	411307101	4804	1447049	SH		Sole		948750		498299
HEALTH CARE
 REIT INC	COM	42217K106	448	9575	SH		Sole		6075		3500
IKANOS COMMU
 NICATIONS	COM	45173E105	15	18000	SH		Sole				18000
ILLUMINA INC	COM	452327109	585	14300	SH		Sole		8600		5700
INCONTACT INC	COM	45336E109	712	206500	SH		Sole		143000		63500
INFUSYSTEM
 HLDGS INC	COM	45685K102	268	281925	SH		Sole		234925		47000
INNER
 WORKINGS INC	COM	45773Y105	1088	138800	SH		Sole		107700		31100
INSIGNIA
 SYS INC	COM	45765Y105	957	405367	SH		Sole		235000		170367
INTEGRAMED
 AMERICA INC	COM NEW	45810N302	2634	337650	SH		Sole		241000		96650
INTERNATIONAL
 BUSINESS MACHS	COM	459200101	812	4644	SH		Sole		3039		1605
INVENTURE
 FOODS INC	COM	461212102	449	116500	SH		Sole		100000		16500
ISIS PHARMA
 CEUTICALS INC	COM	464330109	1352	199450	SH		Sole		124250		75200
JOHNSON &
 JOHNSON	COM	478160104	692	10865	SH		Sole		6040		4825
LAKES
 ENTMNT INC	COM	51206P109	169	69900	SH		Sole		55000		14900
LEMAITRE
 VASCULAR INC	COM	525558201	502	80764	SH		Sole		51210		29554
LILLY ELI & CO	COM	532457108	1081	29250	SH		Sole		18700		10550
LINCOLN EDL
 SVCS CORP	COM	533535100	121	15000	SH		Sole		15000
MEDTOX
 SCIENTIFIC INC	COM NEW	584977201	1067	81500	SH		Sole		27500		54000
MEDTRONIC INC	COM	585055106	536	16124	SH		Sole		10199		5925
METROPOLITAN
 HEALTH NETWRKS	COM	592142103	454	100000	SH		Sole		100000
MIDWAY
 GOLD CORP	COM	598153104	151	75000	SH		Sole				75000
MITEK SYS INC	COM NEW	606710200	231	25000	SH		Sole		25000
MOLSON COORS
 BREWING CO	CL B	60871R209	753	19000	SH		Sole		11250		7750
MULTIBAND CORP	COM NEW	62544X209	1165	473500	SH		Sole		315000		158500
NAVARRE CORP	COM	639208107	1907	1122000	SH		Sole		396500		725500
NETSCOUT
 SYS INC	COM	64115T104	343	30000	SH		Sole		30000
NORTECH SYS INC	COM	656553104	137	45500	SH		Sole		34500		11000
OCULUS INNOVATIVE
 SCIENCES I	COM	67575P108	166	110060	SH		Sole		93060		17000
ONCO
 THYREON INC	COM	682324108	3773	630900	SH		Sole		391100		239800
ORION ENERGY
 SYSTEMS INC	COM	686275108	876	330654	SH		Sole		232754		97900
OWENS
 CORNING NEW	COM	690742101	405	18700	SH		Sole		11150		7550
PFIZER INC	COM	717081103	1525	86231	SH		Sole		36931		49300
PFSWEB INC	COM NEW	717098206	648	171000	SH		Sole		140500		30500
PHARMA
 THENE INC	COM	71714G102	1254	712300	SH		Sole		451200		261100
PHYSICANS FOR
 MULA HLDGS INC	COM	719427106	69	25000	SH		Sole		25000
PLANAR SYS INC	COM	726900103	139	70000	SH		Sole		70000
POLYMET
 MINING CORP	COM	731916102	76	61000	SH		Sole				61000
RADNET INC	COM	750491102	244	100000	SH		Sole		100000
RAINMAKER
 SYSTEMS	COM NEW	750875304	1858	1876656	SH		Sole		1355534		521122
RAMTRON
 INTL CORP	COM NEW	751907304	1186	602091	SH		Sole		404500		197591
RCM TECHN
 OLOGIES INC	COM NEW	749360400	664	150750	SH		Sole		114250		36500
REAL GOODS
 SOLAR INC	CL A	75601N104	43	23700	SH		Sole		11700		12000
RIMAGE CORP	COM	766721104	253	20000	SH		Sole		10000		10000
ROCKWELL
 MEDICAL TECH	COM	774374102	3444	422000	SH		Sole		35000		387000
ROSETTA
 GENOMICS LTD	SHS	M82183118	420	411750	SH		Sole		304250		107500
RTI BIO
 LOGICS INC	COM	74975N105	1888	573950	SH		Sole		381650		192300
SMUCKER J M CO	COM NEW	832696405	716	9825	SH		Sole		7825		2000
SOLTA MED INC	COM	83438K103	61	48854	SH		Sole		27854		21000
ST JUDE MED INC	COM	790849103	2790	77088	SH		Sole		19500		57588
STAAR
 SURGICAL CO	CMPR.01	852312305	3959	507500	SH		Sole		317800		189700
SUMMER
 INFANT INC	COM	865646103	426	64500	SH		Sole		55000		9500
SUPERCONDUCTOR
 TECHNOLOGIES	COM NEW	867931305	160	106500	SH		Sole		102000		4500
SUPERVALU INC	COM	868536103	933	140050	SH		Sole		83400		56650
SYNERGETICS
 USA INC	COM	87160G107	1183	219500	SH		Sole		156500		63000
SYNOVIS LIFE TECH
 NOLOGIES IN	COM	87162G105	5853	350450	SH		Sole		235050		115400
TARGET CORP	COM	87612E106	206	4200	SH		Sole		3000		1200
TCF FINL CORP	COM	872275102	361	39450	SH		Sole		24950		14500
TEARLAB CORP	COM	878193101	173	192308	SH		Sole		192308
TENGION INC	COM	88034G109	153	282685	SH		Sole		247349		35336
TOREADOR
 RES CORP	COM	891050106	123	40000	SH		Sole		40000
TOWERSTREAM
    CORP	COM	892000100	546	213250	SH		Sole		138750		74500
TRANS1 INC	COM	89385X105	1652	550803	SH		Sole		371853		178950
UNITEDHEALTH
 GROUP INC	COM	91324P102	1079	23400	SH		Sole		12900		10500
UQM TECH
 NOLOGIES INC	COM	903213106	124	74250	SH		Sole		53750		20500
UROLOGIX INC	COM	917273104	4875	4924423	SH		Sole		3149598		1774825
UROPLASTY INC	COM	917277204	5465	1126781	SH		Sole		631833		494948
U.S. AUTO PARTS
 NETWORK INC	COM	90343C100	1379	271975	SH		Sole		198525		73450
US BANCORP DEL	COM NEW	902973304	582	24708	SH		Sole		18206		6502
U S PHYSICAL
 THERAPY INC	COM	90337L108	1716	92650	SH		Sole		67050		25600
VERIZON COMMU
 NICATIONS INC	COM	92343V104	262	7113	SH		Sole		4763		2350
VERMILLION INC	COM NEW	92407M206	90	34607	SH		Sole		17607		17000
VOYAGER OIL
 & GAS INC	COM	92911K100	512	243703	SH		Sole		167400		76303
WIRELESS RONIN
 TECHNOLOGIES	COM	97652A203	3451	2556486	SH		Sole		1726107		830379
XILINX INC	COM	983919101	266	9705	SH		Sole		1000		8705
ZIX CORP	COM	98974P100	6353	2379359	SH		Sole		1563948		815411

TOTAL VALUE						141892
DATA RECORDS						131
OTHER MANAGERS ON WHOSE BEHALF REPORT IS FILED		0