The justification of colectomy and ileorectal anastomosis as the primary treatment for familial adenomatous polyposis (FAP) remains questionable because of the rectal cancer risk. We estimated both the cancer risk and the need of rectal excision for benign polyposis in 100 FAP patients. We also evaluated the effects of sulindac therapy and the complications of polyp fulgurations during the follow-up time of the median of 10.6 years (2 to 29 years) after ileorectal anastomosis. There were 46 women and 54 men with a mean age of 32 years (17-67 years) at the operation. Forty-two patients were propositi and 15 had colon cancer primarily. Cumulative risk of rectal cancer and combined risk of cancer and rectal excision for other causes were estimated (Kaplan-Meier analysis) both from the date of surgery and from birth. Nine patients developed rectal cancer, while 12 others has the rectum excised for benign conditions. The cumulative rectal cancer risk was 4%, 5.6%, 7.9% and 25% at 5, 10, 15 and 20 years after the operation, respectively. Rectal excision rates were 7.3%, 13.7%, 23.6%, and 36.6%, correspondingly and finally 73.8%. Age-dependent rectal cancer risks were 3.9%, 12.8% and 25.7% at 40, 50 and 60 years, and the rectal excision rates 9.5%, 26.3% and 44%, respectively. Sulindac caused at least partial regression of rectal adenomas in 71% of patients without major adverse effects, but the long term effects of sulindac and impact on malignant transformation of rectal adenomas are not known. Our results favour proctocolectomy and ileonal anastomosis as the primary operation for FAP instead of colectomy and ileorectal anastomosis.