Transduodenal resection (TDR) of lesions near the ampulla of Vater is an alternative to the Whipple pancreaticoduodenectomy. A retrospective analysis was performed to determine the long-term outcome and the utility of intraoperative frozen section examinations in aiding operative decision making in patients undergoing TDR. From 1992 to 2002, 19 patients with an average age of 64.2 years (range: 33-84 years) underwent a transduodenal resection of a peri-ampullary lesion; median follow-up was 47 months (range: 2-100 months). Pathology of the lesions was as follows: 11 with benign ampullary adenomas, including 4 with familial adenomatous polyposis (FAP); 7 with peri-ampullary adenocarcinomas; and 1 with a benign stricture. Survival for the entire cohort is 100%. In 12 cases an intraoperative frozen section was performed. The specificity and positive predictive value of the intraoperative histology were both 100%, and the sensitivity and negative predictive value were 57% and 38%, respectively. Three of the 4 patients with FAP have recurrent adenomatous change; 2 of the 7 with carcinoma have metastatic adenocarcinoma. Transduodenal resection of peri-ampullary lesions appears to be a safe alternative to radical resection for benign adenomas and selected carcinoma. Intraoperative frozen section assessment is recommended in cases of potential adenocarcinoma.