A 13-year-old girl with Prader-Willi syndrome was admitted to our hospital with an 18-month history of anal bleeding and mucus discharge on defecation. Physical examination revealed obesity, hypogonadism, hypotonia and hypomentia. On digital examination, a nodular mass was palpated on the right wall of the ampulla recti, which was suspected to be carcinoma on a barium enema study. Proctoscopic examination revealed a large, irregular ulceration with white slough at the base, surrounded by the nodular and lumpy mucosa. The lesion was excised by the abdomino-anal pull-through method. The resected specimen showed a lesion of large, shallow, irregular ulcer, 5.0 x 2.2 cm in size. Microscopic examination revealed obliterated lamina propria by fibroblasts and muscle fibers derived from the muscularis mucosae, and misplaced cystic dilated glands in the submucosa at the margin of the ulcer. The gross and microscopic appearances are identical to those of "solitary ulcer of the rectum" described by Madigan and others, and similar to those of "colitis cystica profunda" described by Goodall and others. According to these findings, this lesion was diagnosed as solitary ulcer of the rectum. In the present report, the relationship between solitary ulcer of the rectum and colitis cystica profunda was discussed.