Prophylactic colectomy is generally recommended for patients with familial adenomatous polyposis (FAP) who are inevitably affected with large bowel cancer. After prophylactic colectomy has been performed, gastrointestinal malignancy is the leading cause of death. Duodenal adenomas are found in patients with FAP and the adenoma-carcinoma sequence exists in the FAP duodenum, suggesting that treatment of duodenal polyps might be beneficial. Several methods of treatment for duodenal lesions in patients with FAP have been reported, but the current treatment options are not ideal. The nonsteroid anti-inflammatory drugs, sulindac and aspirin, are used for chemoprevention, while recently developed cyclooxygenase-2 inhibitors may be of some use in the future. Endoscopic polypectomy has been attempted for duodenal polyps and open surgical polypectomy has proven to be effective for selected patients. Photodynamic therapy and Argon plasma coagulation may be suitable to treat carpeted polyposis. New methods of duodenal resection, such as pancreas-preserving duodenectomy and pylorus-preserving pancreaticoduodenectomy, might be considered for severe duodenal polyposis; however, because prophylactic duodenal surgery has been considered too aggressive, surveillance duodenoscopy is usually performed to detect duodenal cancer at an early stage.