We report a case of gastrointestinal stromal tumor (GIST) with perforation in the jejunum and peritoneal dissemination. A 64 year-old man admitted our hospital with severe abdominal pain. He had findings of panperitonitis and the abdominal CT examination revealed free air and an intraabdominal abscess. We suspected perforation of the small intestine and operated. There were two adjacent tumors (6cm in diameter each) of the jejunum and peritoneal dissemination, and one of them was perforated. We performed a jejunojejunostomy and resected as all disseminated tumors as possible. Histopathological findings showed that the tumors were composed of spindle cell proliferation with three or four mitoses per high-power fields (HPF). Because tumor cell were positive for c-kit and CD34, and negative for alpha-smooth muscle actin and S-100 immunohistochemically, we diagnosed these tumors as “maligmant GIST of small intestine, uncommitted type”. Perforation of GIST is rare. Only 20 cases of GIST with peritonitis due to perforation have been reported in Japan, including the present case. Of 20 cases, 14 were small intestinal GIST. Small intestinal GIST should be recognized as a high-risk group of malignancy and perforation.