We report an unusual case of anorectal agenesis with a rectourethral fistula diagnosed in a 48-year-old man. The patient presented after noticing hematuria, although he had been aware of urinary leakage from his colostomy with occasional fecal urine for about 4 years. He had had a double-barrel colostomy created soon after birth for an imperforate anus, with revision at the age of 4 years to correct a prolapse of the stoma, but his malformation had never been repaired. We performed a physical examination, which did not reveal a perineal fistula, but urethrocystography demonstrated high anorectal agenesis with a rectourethral fistula. Thus, we resected the rectourethral fistula and created an end-colostomy. The patient had an uneventful postoperative course, and was discharged in good health on postoperative day 19. To our knowledge, this is the oldest patient to be diagnosed with anorectal agenesis and undergo resection of a rectourethral fistula.