Abstract: Objective To analyze the characteristics of the clinicopathology and genotypes in patients with gastrointestinal stromal tumor (GIST). Methods The clinicopathological and genotypic data of 179 patients with GIST, who underwent treatment and genetic testing in the Hostital of West China from September 2009 to February 2009 were collected retrospectively. Results The tumor sites of the cases were located in stomach (88 cases, 49.2%), small intestine (70 cases, 39.1%), colorectum (7 cases, 3.9%) and the other sites (14 cases, 7.8%) respectively. 94.4%, 74.9% and 93.3% of GIST patients were positive for CD117, CD34 and DOG-1 immunophenotypes respectively.c-kit and PDGFRαmutations were found in 151 cases (84.4%) and 8 cases (4.5%) except for the wild types of the rest 20 cases (11.2%). Among all thec-kit mutation, 92.2% mutation types in exon 11 were deletion mutation, point mutation and hybrid mutations, and in exon 9 the mutation types were just involving A502_Y503dup (n=6) and Y403_F504ins (n=14), while the mutation type were K642Q in exon 13 (n=1) and N822K in 17 (n=2). There were 6 patients with the mutation types of PDGFRαin exon 18, and 3 of them were type of D842V. In the GIST genotyping, DOG-1 positive rate in PDGFRαmutation patients were significantly lower than that inc-kit mutation and wild type patients ( P=0.007). In the various type ofc-kit mutations, the positive rate of CD34 in point mutation patients were significantly lower than that in other mutation types ( P<0.001). The rate of high-risk patients in point mutation and insertion mutation patients were lower than that in deletion mutation and deletion + insertion mutation patients ( P=0.006). Conclusion The most common localizaions of GISTs are the stomach and small intestine. The most frequent mutation type of GIST isc-kit exon 11. The individualized treatment is required for GIST patients because its high mutation rate and types.