Pneumatosis cystoides intestinalis is a condition in which polycystic air has entered the submucosa or serosa of the intestine. A 78-year-old man was admitted to our hospital for treatment of end-stage renal disease due to diabetic nephropathy. Peritoneal dialysis was initiated on hospital Day 14. We diagnosed peritonitis and the patient was treated with vancomycin on Day 40. However, computed tomography showed hepatic portal venous gas and dilation of the small intestine with pneumatosis on Day 55, and the patient subsequently died. Autopsy revealed multiple mucosal pneumatoses, up to 1 cm in diameter, from the duodenum to jejunum, which was consistent with pneumatosis cystoides intestinalis. No cystic lesions were found in the colon. Pneumatosis cystoides intestinalis is a rare and usually benign disorder, but in patients with diabetic end-stage renal disease, it may run a malignant course, perhaps due to uremic immune incompetence.