Objective To investigate the expression of immunophenotype in gastrointestinal stromal tumors and analyze its clinical value in the diagnosis and prognosis of gastrointestional stromal tumors.Methods Reviewed the clinical data of 323 patients with gastrointestinal stromal tumors in Fuzhou General Hospital of PLA from January 2004 to January 2014.Detected expressions of CD-117,DOG-1,CD-34,alpha-SMA,S-100.Desmin and Ki-67 by immunohistochemical S-P method,frequency statistics,independent sample t test and correlation analysis was carried out with SPSS 20.Results The positive rates of CD-117,DOG-1 and GIST in the group CD-34 were 97％,95.6％ and 86％ respectively,the positive rates of alpha-SMA,S-100 and Desmin were 59.8％,27.7％ and 17％ respectively,the positive expression of CD-117,CD-34,alpha α-SMA and Desmind in intestinal gastrointestinal stromal tumors and gastric gastrointestinal stromal tumors were significantly different,among them (P ＜ 0.05),the positive rates of gastrointestinal stromal tumors and alpha-SMA in intestinal CD-117 were significantly higher than those in gastric gastrointestinal stromal tumors (3.37 vs 2.99,P =0.002;1.59 vs 1.09 P =0.005).The positive expression of CD-34 and Desmin was significantly lower than that of gastric gastrointestinal stromal tumors (1.90 vs 3.02,P =0.000;0.12 vs 0.50,P =0.001).The expression of CD-117 was significantly correlated with location and risk grade (P =0.000,0.002).The expression of DOG-1 was significantly correlated with the risk grade,and the overall survival (P ＜0.05).The expression of CD-34 was significantly correlated with location,size,risk grade,status,and overall survival (P =0.000,0.007,0.016,0.001).There was a significant correlation between the expression of alpha-SMA and location (P =0.036).There was a significant correlation between the expression of S-100 and the overall survival (P =0.036).The expression of Desmin was significantly correlated with the age and location of the first visit (P =0.001).Conclusion In the diagnosis of gastrointestinal stromal tumors,CD-117,DOG 1 and CD-34 combined alpha-SMA and Desmin have good complementation,it is also helpful to judge the location of the intestine and stomach of gastrointestinal stromal tumors,if necessary,it can also be detected by gene mutation,with reference to the level of mitotic figures,which can reduce the misdiagnosis rate and increase the detection rate.