To explore the relationship between c-kit and platelet-derived growth factor receptor alpha(PDGFRA) gene mutation features and the prognosis of gastrointestinal stromal tumor(GIST). Clinicopathological, genetic testing and follow-up informations of patients admitted to the Shanxi Tumor Hospital from June 2000 to January 2009 were collected. The survival was calculated and univariate analysis was conducted using the Kaplan-Meier method. Multivariate analysis was conducted by the Cox regression method. The 5-year disease-free survival rate was 61.5% and the 5-year overall survival rate was 67.4%. The 5-year disease-free survival rates of patients without disease among those with c-kit exon 11 mutation (n=77), c-kit exon 9 mutation(n=4), and PDGFRA exon 18 mutation (n=2) were 63.4%, 14.3% and 100%, and the 5-year overall survival rates were 70.8%, 50.0% and 100%, respectively. In the patients with c-kit exon 11 mutation, the 5-year disease-free survival rates among those with point mutations(n=26), deletion mutations(n=44), and duplication mutations(n=7) were 87.1%, 44.9% and 80.0%, and the 5-year overall survival rates were 88.1%, 57.0% and 100%, respectively. There were significant differences in overall survival among different factors. Multivariate analysis showed that gene mutation was not the independent factor of prognosis(P=0.492). In GIST patients undergoing surgery without imatinib treatment, mutated genotype is better than wild type in terms of prognosis. Gene mutation is not the independent factor of prognosis in GIST patients.