Form 13F

Form 13F COVER PAGE

Report for the Calendar Year or Quarter Ended:  31-Mar-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, 5/9/2012

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).)






													VOTING AUTHORITY
			TTL OF		VALUE	SHARES/	SH/	PUT/	INV	OTR
NAME OF ISSUER	CLASS	CUSIP		x1000	PRN AMT	PRN	CALL	DISC	MGRS	SOLE	SHRD	NONE
ABBOTT LABS		COM	002824100	1264	20625		SH		Sole		13275		7350
ACTUATE CORP	COM	00508B102	1844	293700	SH		Sole		210000	83700
AEGION CORP		COM	00770F104	590	33100		SH		Sole		15600		17500
AFLAC INC		COM	001055102	699	15200		SH		Sole		9350		5850
ALPHATEC
 HOLDINGS INC	COM	02081G102	1110	468150	SH		Sole		401900	66250
ALTRIA GROUP INC	COM	02209S103	409	13250		SH		Sole		12750		500
AMERICAN WTR
 WKS CO INC NEW	COM	030420103	476	14000		SH		Sole		9700		4300
ANGEION CORP	COM	03462H404	172	30000		SH		Sole		30000
APPLIANCE RECYC
 LING CTRS AME	CMNW	03814F205	3942	849478	SH		Sole		589750	259728
ARABIAN
 AMERN DEV CO	COM	038465100	96	10300		SH		Sole		10300
ARRAY
 BIOPHARMA INC	COM	04269X105	1062	311750	SH		Sole		265500	46250
ASPENBIO
 PHARMA  INC	CMNW	045346202	1211	1659299	SH		Sole		1044400	614899
AT&T     INC	COM	00206R102	322	10312		SH		Sole		8312		2000
ATRICURE INC	COM	04963C209	1833	184200	SH		Sole		136250	47950
AUTHENTEC INC	COM	052660107	250	79000		SH		Sole		74000		5000
AVI BIOPHARMA INC	COM	002346104	2650	1720500	SH		Sole		1216300	504200
BACTERIN INTL
 HLDGS   INC	COM	05644R101	528	218000	SH		Sole		205500	12500
BAXTER INTL INC	COM	071813109	1425	23840		SH		Sole		16540		7300
BIOSCRIP INC	COM	09069N108	594	87500		SH		Sole		79625		7875
BRIDGELINE
 DIGITAL INC	COM	10807Q205	69	61000		SH		Sole		26000		35000
BRISTOL MYERS
 SQUIBB   CO	COM	110122108	1672	49550		SH		Sole		32050		17500
CALIX    INC	COM	13100M509	268	31387		SH		Sole		5371		26016
CARDICA  INC	COM	14141R101	1627	760011	SH		Sole		643113	116898
CARDIOME
 PHARMA CORP	CMNW	14159U202	49	70000		SH		Sole		70000
CARDIONET INC	COM	14159L103	1144	371401	SH		Sole		320151	51250
CARDIOVASCULAR
 SYS INC DEL	COM	141619106	2530	273550	SH		Sole		146300	127250
CHEVRON CORP NEW	COM	166764100	618	5760		SH		Sole		3700		2060
COLEMAN CABLE INC	COM	193459302	595	61170		SH		Sole		50070		11100
COMPUTER TASK
 GROUP   INC	COM	205477102	1578	103000	SH		Sole		91500		11500
CONCEPTUS INC	COM	206016107	220	15300		SH		Sole		8200		7100
CVS CAREMARK
 CORPORATION	COM	126650100	724	16150		SH		Sole		10600		5550
CYTORI
 THERAPEUTICS INC	COM	23283K105	1582	635250	SH		Sole		384250	251000
DATALINK CORP	COM	237934104	1937	203450	SH		Sole		134350	69100
DELUXE  CORP	COM	248019101	843	35975		SH		Sole		26025		9950
DEXCOM   INC	COM	252131107	405	38800		SH		Sole		22700		16100
DIGIRAD CORP	COM	253827109	814	387580	SH		Sole		342880	44700
DONALDSON INC	COM	257651109	1172	32800		SH		Sole		18800		14000
DOT HILL SYS CORP	COM	25848T109	1651	1093055	SH		Sole		885555	207500
EBIX     INC	CMNW	278715206	926	40000		SH		Sole		40000
ECHO GLOBAL
 LOGISTICS INC	COM	27875T101	837	52000		SH		Sole		35500		16500
ECOTALITY INC	CMNW	27922Y202	165	168000	SH		Sole		122500	45500
EDAP TMS S A 	SPDR	268311107	1922	1011500	SH		Sole		783500	228000
ELECTROMED INC	COM	285409108	818	282000	SH		Sole		242000	40000
ENDOLOGIX INC	COM	29266S106	4783	326469	SH		Sole		227069	99400
EPLUS    INC	COM	294268107	1423	44500		SH		Sole		37000		7500
EXACT
 SCIENCES CORP	COM	30063P105	953	85400		SH		Sole		54400		31000
FAMOUS DAVES
 AMER    INC	COM	307068106	1625	140050	SH		Sole		86300		53750
GENERAL MLS INC	COM	370334104	237	6012		SH		Sole		4012		2000
GLAXO
 SMITHKLINE PLC	SPDR	37733W105	678	15100		SH		Sole		8950		6150
GLOBECOMM
 SYSTEMS INC	COM	37956X103	1735	119853	SH		Sole		100753	19100
GRANITE CITY
 FOOD & BREWERY	CMNW	38724Q404	94	42082		SH		Sole		333		41749
GSV CAP CORP	COM	36191J101	1319	70550		SH		Sole		47650		22900
HANSEN
 MEDICAL INC	COM	411307101	4602	1534050	SH		Sole		1098950	435100
HEALTH CARE
 REIT    INC	COM	42217K106	515	9375		SH		Sole		5925		3450
INCONTACT INC	COM	45336E109	1155	206975	SH		Sole		197475	9500
INFUSYSTEM
 HLDGS   INC	COM	45685K102	1999	1030199	SH		Sole		928199	102000
INNERWORKINGS INC	COM	45773Y105	1609	138100	SH		Sole		108000	30100
INSIGNIA SYS INC	COM	45765Y105	489	270367	SH		Sole		100000	170367
INTEGRAMED
 AMER    INC	CMNW	45810N302	3514	290300	SH		Sole		225700	64600
INTERNATIONAL
 BUSINESS MACHS	COM	459200101	969	4644		SH		Sole		3214		1430
INVENTURE
 FOODS   INC	COM	461212102	503	101500	SH		Sole		87000		14500
ISIS PHARMA
 CEUTICALS INC	COM	464330109	1062	121100	SH		Sole		81100		40000
JOHNSON & JOHNSON	COM	478160104	718	10890		SH		Sole		6390		4500
JONES SODA CO	COM	48023P106	773	1684500	SH		Sole		1450500	234000
LAKES ENTMNT INC	COM	51206P109	117	64900		SH		Sole		55600		9300
LEMAITRE
 VASCULAR INC	COM	525558201	435	73914		SH		Sole		62614		11300
LILLY ELI & CO	COM	532457108	1218	30250		SH		Sole		19400		10850
LINCOLN EDL
 SVCS   CORP	COM	533535100	119	15000		SH		Sole		15000
MEDTOX
 SCIENTIFIC INC	CMNW	584977201	1374	81500		SH		Sole		30500		51000
METROPOLITAN
 HEALTH NETWORKS	COM	592142103	937	100000	SH		Sole		100000
MICROSOFT CORP	COM	594918104	1123	34825		SH		Sole		21175		13650
MIDWAY GOLD CORP	COM	598153104	107	75000		SH		Sole				75000
MOLSON COORS
 BREWING  CO	CL B	60871R209	860	19000		SH		Sole		11450		7550
MULTIBAND CORP	CMNW	62544X209	861	286000	SH		Sole		188500	97500
NAVARRE CORP	COM	639208107	2120	1191000	SH		Sole		434000	757000
NETSCOUT SYS INC	COM	64115T104	610	30000		SH		Sole		30000
NEUROMETRIX INC	CMNW	641255203	148	200000	SH		Sole		170000	30000
NORTECH SYS INC	COM	656553104	158	38000		SH		Sole		34500		3500
NOVADAQ
 TECHNOLOGIES INC	COM	66987G102	655	100000	SH		Sole		92750		7250
OCULUS INNOVATIVE
 SCIENCES  I	COM	67575P108	89	67000		SH		Sole		52000		15000
ONCOTHYREON INC	COM	682324108	2694	617951	SH		Sole		386401	231550
ORION ENERGY
 SYSTEMS INC	COM	686275108	1407	591145	SH		Sole		513945	77200
OWENS CORNING NEW	COM	690742101	638	17700		SH		Sole		10400		7300
PFIZER   INC	COM	717081103	1651	72926		SH		Sole		31781		41145
PFSWEB   INC	CMNW	717098206	55	14000		SH		Sole		14000
PHARMATHENE INC	COM	71714G102	1466	828400	SH		Sole		516000	312400
PHYSICANS FORMULA
 HLDGS   INC	COM	719427106	75	25000		SH		Sole		25000
PLANAR SYS INC	COM	726900103	168	70000		SH		Sole		70000
POLYMET
 MINING CORP	COM	731916102	71	61000		SH		Sole				61000
PROSHARES TR II	DJCR	74347W650	1515	35300		SH		Sole		24800		10500
RAINMAKER
     SYSTEMS	CMNW	750875304	1826	2200584	SH		Sole		1882584	318000
RAMTRON INTL CORP	CMNW	751907304	1198	602091	SH		Sole		520091	82000
RIMAGE  CORP	COM	766721104	433	43300		SH		Sole		27300		16000
ROCKWELL
 MEDICAL TECH 	COM	774374102	3992	422000	SH		Sole		35000		387000
ROYAL DUTCH
 SHELL   PLC	SPADR	780259107	579	8200		SH		Sole		4950		3250
RTI BIO
 LOGICS  INC	COM	74975N105	1879	507900	SH		Sole		430600	77300
SANOFI      	SPADR	80105N105	775	20000		SH		Sole		13450		6550
SEQUENOM INC	CMNW	817337405	250	61500		SH		Sole		39000		22500
SMUCKER J M CO	CMNW	832696405	807	9925		SH		Sole		7925		2000
ST JUDE MED INC	COM	790849103	3416	77088		SH		Sole		19500		57588
STAAR
 SURGICAL CO	CP.01	852312305	4052	374100	SH		Sole		229700	144400
STAPLES  INC	COM	855030102	771	47600		SH		Sole		28850		18750
SUPERCONDUCTOR
 TECHNOLOGIES	CMNW	867931305	130	167262	SH		Sole		165262	2000
SUPERVALU INC	COM	868536103	644	112800	SH		Sole		75800		37000
SYNERGETICS
 USA     INC	COM	87160G107	1372	211000	SH		Sole		148500	62500
SYNERGY RES CORP	COM	87164P103	332	99000		SH		Sole		95000		4000
TARGET  CORP	COM	87612E106	230	3950		SH		Sole		3550		400
TEARLAB CORP	COM	878193101	861	253163	SH		Sole		243163	10000
TENGION  INC	COM	88034G109	10	17668		SH		Sole				17668
TOWERSTREAM CORP	COM	892000100	219	46000		SH		Sole		27000		19000
TRANS1   INC	COM	89385X105	2676	729153	SH		Sole		548653	180500
UNITEDHEALTH
 GROUP   INC	COM	91324P102	1379	23400		SH		Sole		13250		10150
UQM TECH
 NOLOGIES INC	COM	903213106	104	70000		SH		Sole		59500		10500
UROLOGIX INC	COM	917273104	6961	5437950	SH		Sole		3513300	1924650
UROPLASTY INC	CMNW	917277204	3291	1093281	SH		Sole		616933	476348
U.S. AUTO PARTS
 NETWORK INC	COM	90343C100	195	54075		SH		Sole		47075		7000
US BANCORP DEL	CMNW	902973304	753	23760		SH		Sole		17890		5870
U S PHYSICAL
 THERAPY INC	COM	90337L108	2046	88750		SH		Sole		65150		23600
VERIZON COMMU
   NICATIONS	COM	92343V104	272	7113		SH		Sole		7113
VOYAGER OIL
 & GAS   INC	COM	92911K100	938	385828	SH		Sole		354919	30909
WIRELESS RONIN
 TECHNOLOGIES	COM	97652A203	2567	2883799	SH		Sole		2343675	540124
XILINX   INC	COM	983919101	354	9705		SH		Sole		9705
ZIX     CORP	COM	98974P100	4218	1449641	SH		Sole		986742	462899