Most small bowel polyps in familial adenomatous polyposis (FAP) occur in the peri-ampullary region, and distal small bowel adenomas and carcinomas are comparatively less common. As standard therapy in FAP consists of proctocolectomy with ileal pouch anal anastomosis, or ileorectal anastomosis, it is essential to be aware of the potential for adenomatous polyp formation in the terminal ileum and rectum. Ileal adenomas are found in 9-20% of patients with FAP, and new polyps may develop after colectomy. Ileal lymphoid hyperplasia and polyps are 2-4 times more common than adenomas, may be indistinguishable from adenomas on examination (requiring biopsy for diagnosis), and tend to regress after colectomy. Adenomas may arise in pouches, usually after an interval of several years, and have been documented to occur in the terminal ileum up to 25 years after colectomy. At pouch construction, rectal mucosectomy may theoretically fail to remove all mucosa at risk. Small islets of rectal mucosa may remain after this technically difficult operation, and the late development of cancer, up to 20 years postoperation has been noted. A stapled anastomosis may arguably have a better physiological result, but a greater amount of residual rectal mucosa may increase late cancer risk. Annual endoscopic follow-up of pouches is recommended. All polyps or suspicious lesions should be biopsied, excised or destroyed, preserving a sample for histology. After ileorectal anastomosis, cancer risk in the rectal stump increases with chronological age, with risk ranging from 5-10% at age 50 years, to 14-29% at age 60 years. Surveillance of the rectal stump in FAP is recommended every 4-6 months. There may be a role for prostaglandin synthesis inhibitors in some patients.