The authors reviewed the case records of 1050 familial adenomatous polyposis (FAP) patients who were registered at their institution. The organ-specific morbidity and mortality rates of malignant tumor in FAP patients were compared with those of the general population of Japan, and the prognosis after rectum-preserving operation also was calculated. The cumulative prevalence of colorectal carcinoma at the age of 44 years was 0.52 for men and 0.61 for women. The observed/expected morbidity ratio was 20.9 (95% confidence interval, 10.8-36.6) for thyroid carcinoma, 3.08 (2.03-7.75) for gastric carcinoma, and 295 (263-330) for colorectal carcinoma. The observed/expected mortality ratios was 250 (112-447) for periampullary and small intestinal carcinoma, 3.43 (1.77-6.0) for gastric carcinoma, and 210 (183-241) for colorectal carcinoma. The risk of rectal carcinoma after ileorectal anastomosis was 13% (8.5-17.5%) at 10 years and 37% at 20 years. The results clarified the impact of FAP on the carcinogenesis in several organs as a whole including preserved rectum, and suggested a direction of the rational treatment of FAP.