The aim of this study was to evaluate the long-term prognosis of patients who underwent colectomy for familial adenomatous polyposis. The clinical data of 29 familial adenomatous polyposis patients who underwent colectomy were retrospectively reviewed. Five patients died of causes that included colorectal cancer (CRC), desmoid tumor, cancer of the small intestine, and pancreatitis. The 30-year survival rate was 72%. Among the 15 patients who had CRC at primary surgery, the 5-year survival rate was 100% in stages 0, I, and II, and 75% in stage IIIA. Stage I desmoid tumor showed slow or no growth, whereas a stage IV tumor showed rapid growth and was fatal. Extracolonic malignancies were seen in the small intestine, stomach, duodenum, thyroid, kidney, breast, and ovary. Among 8 patients with ileorectal anastomosis, 4 had a second primary rectal cancer and 6 had a salvage reoperation. None of the patients who underwent either stapled or handsewn ileal pouch–anal anastomosis had second primary rectal cancers. The stage of primary CRC at colectomy is the most important prognostic factor. But in addition to second primary CRC, the management of desmoid tumors and extracolonic malignancies is important for long-term survival regardless of the anastomotic technique used.