A 79-year-old woman with bloody diarrhea was diagnosed with ulcerative colitis. She developed intestinal perforation after high-dose steroid therapy. An emergency laparotomy revealed a perforation in the ascending colon, and a subtotal colectomy was performed with an ileostomy and a mucous fistula in the sigmoid colon. Histological findings of the resected colon showed the presence of cytomegalovirus in the endothelial cells of vessels around the ulcer floor. Twelve days after the laparotomy, she developed an ileal perforation with a bloody discharge from the ileostomy and underwent an emergency laparotomy. Multiple intestinal perforations were found in the ileum, and the perforated ileum was resected. Cytomegalovirus infection was controlled with ganciclovir postoperatively. Histological findings of the resected ileum showed the presence of cytomegalovirus in the endothelial cells of vessels around the ulcer floor. This is the first report of ileal perforation due to cytomegalovirus infection confirmed pathologically in a patient with ulcerative colitis. © Springer 2013.