Purpose Adenocarcinomas of the ampulla of Vater demonstrate a characteristic histology but vary significantly in outcome. As a consequence, prognostic factors for these cancers are poorly defined. The caudal-type homeodomain transcription factors 1 (CDX1) and 2 (CDX2) regulate axial development and intestinal differentiation. We assessed the expression of these putative intestinal epithelial-specific transcription factors and their influence on patient outcome. Patients and Methods Fifty-three resected carcinomas of the ampulla of Vater, 31 pancreatic ductal adenocarcinomas, and 15 extrahepatic biliary carcinomas were analyzed for CDX1 and CDX2 expression using immunohistochemistry. Results Forty percent of carcinomas of the ampulla of Vater but less than 5% of pancreatic and biliary adenocarcinomas expressed CDX Expression of CDX was associated with a better prognosis (P=.0009). Individually, both CDXI (P=.02) and CDX2 (P=.02) expression were associated with a survival advantage on univariate analysis. Advanced T stage (P=.02), lymph node metastases (P=.004), and vascular space invasion (P=.0009) were associated with a poor prognosis. Multivariate analysis revealed vascular space invasion (P=.01) and CDX expression (P=.01) to be independent prognostic factors. Conclusion Expression of CDX was an independent marker of outcome in patients with resected adenocarcinoma of the ampulla of Vater. Expression of CDX may distinguish good prognosis intestinal-like tumors, which potentially arise within intestinal epithelium, from poorer prognosis pancreatobiliary tumors, which arise in adjacent pancreatic and/or biliary ductal epithelium. (c) 2005 by American Society of Clinical Oncology.