A 30-year-old man was diagnosed to have a large intra-abdominal tumor in 1999. A histological examination of a resected liver specimen from an operation in 2002 revealed a gastrointestinal stromal tumor (GIST), diagnosed based on positive immunostaining for CD34 and c-kit. Two years after the operation, new lesions developed in the residual liver and the lesser curvature of the stomach. An immunohistological examination of both specimens showed the features of a GIST, thus matching those of the first histological examination of the liver GIST. While there were no mutations at exon 11 of c-kit in the liver GISTs resected in 2002 and 2004, the gastric lesion had a mutation at P577L (CCT to CTT) at exon 11. Therefore, the liver GIST and the gastric lesion were diagnosed to be independent. The patient already has survived for more than 9 years after receiving surgery three times and with administration of imatinib.