Duodenal and ampullary carcinoma in familial adenomatosis (FAP) is the third leading cause of FAP related deaths. Management of this condition is a challenging. The aim of this study was to evaluate the role of multiple targeted endoscopic biopsies and macroscopic appearance as the major determinants for surgical intervention. A secondary aim was to assess histological heterogeneity through comparing endoscopic biopsies and describe the clinical outcomes of our cohort after intervention. We reviewed our FAP surveillance database of 67 patients, between January 1999--June 2011 undergoing upper GI surveillance and where indicated, subsequent surgical intervention. Among 67 patients, 11 underwent surgical resection. Pancreas-preserving duodenectomy was performed in four patients (five procedures), and Whipple's operation in seven patients. The average size of polyps was 43 mm (range 17-65 mm), and the average number of targeted endoscopic biopsies per lesion was 7.5 (range 5-10). Two cases of high-grade (severe) dysplasia were diagnosed on endoscopic biopsies each understaged compared with the subsequent surgical specimen. All carcinomas identified have been resectable with no evidence of local spread or distant metastasis. There was one postoperative death, but no cancer related deaths. We identified both cancers at an early stage and there were no missed or late diagnoses. There have been no recurrences of carcinoma in a more than 7 years follow-up. Due to the heterogeneous nature of these lesions, comprehensive macroscopic assessment should be complemented with multiple targeted biopsies to improve the chance of early detection of advanced lesions.