We report a case of a large gastrointestinal stromal tumor (GIST), greater than 5 cm in diameter, in the stomach. Microscopically, high levels of mitosis were observed, indicative of a high-grade malignancy. We analyzed the c-kit gene mutations by a replication competent retrovirus assay and DNA sequencing, which revealed a c-kit mutation in exon 11. Liver metastases were detected 7 months after surgery. Patients with an exon 11 mutation of the c-kit gene are reported to have a high response to STI571 (imatinib mesylate, Glivec). Accordingly, a 1-month course of STI571 treatment clearly changed the characterization of the metastatic tumors radiographically. Thus, it may be important to analyze c-kit gene mutations in patients presenting with GISTs to predict the effectiveness of STI571 in suppressing GISTs, especially tumors thought to have malignant potential.