We report a case of anal canal cancer complicated with anal stricture, which was diagnosed 22 years after the onset of Crohn's disease. The patient was a 60-year-old man, who developed Crohn's disease in the small and large intestines in 1980 at the age of 27. In 1990, he developed an inflammatory mass in the ileum, and underwent a right hemicolectomy. In April 2002, 22 years after the onset of Crohn's disease, he was admitted to our hospital because of anal pain and bowel obstruction. Imaging studies indicated a fistula between the ileo-transverse colonic anastomosis and the small bowel. He also developed anal pain and stricture with an induration, which was diagnosed with well differentiated adenocarcinoma based on histological examination of biopsy specimen obtained under spinal anesthesia. In May 2002, he underwent an abdominoperineal resection of the rectum, sigmoid colostomy, the resection of the ileo-transverse colonic anastomosis and small bowel strictureplasty. In April 2004, he developed a peristomal abscess, and required removal of the residual colon and ileostomy construction. At present, there are no signs of cancer recurrence. A careful anal examination is indispensable in Crohn's disease patients with anal stricture because of the potential risk of developing anal canal cancer.