Introduction: Recent advance in understanding the biology of gastrointestinal stromal tumor (GIST) etiology involves specifically recognizing the central role of activating KIT mutation and associated KIT protein expression in these lesions. This has led to the development of novel, effective GIST therapy using the receptor tyrosine kinase inhibitor imatinib. We reviewed cases diagnosed pathologically as GIST based on diagnostic criteria. Methods: We reviewed data from patients histologically diagnosed with GIST between 1996 and 2005. Results: We found 31 primary GISTs, 14 recurrent GISTs and 22 small incidental GISTs incidentally during surgery for other diseases. Among primary GISTs, we found 18 cases (58.1%) in the stomach and 17 (54.8%) that were asymptomatic. Most small incidental GISTs were 5-10 mm in size and considered low-risk due to findings of mitosis and MIB-1 index. Although 10 cases involving 14 recurrent GISTs were resected surgically, six recurred, imatinib was administered to 7 patients and was effective in four. One case showed complete response lasting over five years. Conclusions: Asymptomatic GISTs may be often found incidentally in routine health checkup examination in Japan. Therefore, tumor size of GISTs in Japan tends to smaller than that in western countries. Before the development of imatinib, some patients with recurrence underwent tumor resection. Imatinib now has priority in treating recurrent GISTs, and surgery should be considered only for local recurrence or liver metastasis that is completely resectable.