Abdominal ultrasonography revealed a low echoic mass in the upper abdomen of a 65-year-old man. He was referred to our department, where abdominal CT revealed a tumor with a 30-mm contrast effect on the distal side of the inferior part of the duodenum. Endoscopy revealed a submucosal tumor in the same region, and ultrasonic endoscopy showed a low echoic mass with a clear boundary derived from the muscle layer. The duodenum was partially resected based on a diagnosis of suspected gastrointestinal stromal tumors (GIST), and the skin tumor was simultaneously resected. An elastic, soft, 30-mm tumor mass was found in the upper duodenum during surgery, and small nodules of 3-5mm were identified throughout the 110-cm length of the jejunum at intervals of 20-30cm. The histopathological diagnosis was GIST and immunostaining showed the mass to be c-kit and CD34 positive. We diagnosed the skin tumor as a neurofibroma (von Recklinghausen disease). Mutational analysis of c-kit in the resected specimen showed no mutation, therefore suggesting that imatinib would not be effective. Since the nodules remaining in the small intestine might also be GIST, we established a policy of regular imaging assessments.