A 39-year-old man was brought into the emergency department in our hospital because of abdominal pain and abdominal distention. Computed tomography revealed abdominal fluid and a 20×20×6cm giant polycystic tumor at the backward of the stomach. After an emergency angiography and an embolization at the left gastric artery, the patient was admitted. No defenite diagnosis was made with ultrasonography, gastrointestinal endoscopy, endoscopic retrograde cholangiopancreatography, enhanced abdominal computed tomography and magnetic resonance imaging. Resection of the tumor with a partial resection of the stomach was performed. Leiomyosarcoma of the stomach was suspected by postoperative histopathological examination. But the tumor was definitely diagnosed as gastrointestinal stromal tumor in immunostaining. We infered that the growth of the tumor with polycystic change might be due to the intramural bleeding of the tumor. It seems to be extremely rare that gastrointestinal stromal tumor with polycystic change occurs, and so we report this case together with some bibliographical comments.