We report a patient with synchronous gastrointestinal stromal tumors (GISTs) of the stomach and esophagus. The gastric GIST was larger than that in the esophagus, and no direct connection between the two lesions was seen microscopically. Based on molecular analysis, both lesions had the same c-kit mutation on exon 11, with deletion of codon 557-558. Analysis of normal gastric tissue showed no mutations. The gastric GIST was the primary lesion, and the esophageal tumor was thought to suggest a hematogenous metastasis. A liver metastasis in S6 appeared 6 months after surgery. Imatinib mesylate has been an effective treatment for liver metastasis at follow-up of 2 years.