This study included 89 patients with GIST who had a resection between January 1991 and March 2009. The clinicopathological features of the 62 cases with gastric tumors and the 27 cases with small intestinal tumors were compared. The following 11 factors were examined : clinical symptoms, sex, age, tumor size, presence of ulcer, growth pattern, mitotic index, risk classification, tumor metastasis, concomitant neoplasm, and recurrence-free survival. There were no differences between gastric GIST and small intestinal GIST patients in any of the factors except clinical symptoms. During follow up, (median 30.5 months) 20 patients had a recurrence and 19 patients had a concomitant neoplasm. The overall recurrence-free survival was 73.1% at 5 years and 64.3% at 10 years. The 10-year recurrence-free survival for gastric GIST patients was 69.7% and it was 52.1% for small intestine GIST patients. The prognosis of small intestinal GIST patients was not significantly lower compared to gastric GIST patients (p=0.167). Univariate analysis of the clinicopathological factors showed that recurrence-free survival was significantly correlated with tumor size and mitotic index. Multivariate analysis using a Cox proportional hazards model identified tumor size (>50 mm) and mitotic index (>6) as significant independent risk factors for recurrence-free survival.