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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.