Most adenomas and carcinomas of small intestine and extrahepatic bile ducts arise in the region of Vater's papilla. In FAP it is the main location for carcinomas after proctocolectomy. In many cases symptoms due to stenosis lead to diagnosis in an early tumor stage. In about 80% curative intended resection is possible. Operability is the most relevant prognostic factor. Inflammatory changes, fibrosis, regeneratory changes after endoscopic manipulation, hyperplasia, preneoplastic lesions close to carcinoma, deeply sited carcinomas under protruded, non-neoplastic duodenal mucosa make the diagnosis difficult on biopsy material. Histologically, intestinal type adenocarcinoma, pancreatobiliary type adenocarcinoma, undifferentiated carcinomas and unusual types can be differentiated. In our own series comprising 45 resected ampullary carcinomas 6 from 10 intestinal type adenocarcinomas, and 4 carcinomas of unusual types expressed the immunohistochemical marker profile of intestinal mucosa (keratin 7-, keratin 20+, MUC2+). 17 from 21 pancreatobiliary type adenocarcinomas, 4 undifferentiated carcinomas, as well as 3 papillary carcinomas showed the immunohistochemical profile of pancreaticobiliary duct mucosa (keratin 7+, keratin 20-, MUC2-). 3 invasive carcinomas which were negative for these markers, showed one of these characteristic marker-combinations in non-invasive adenomatous parts. These findings support the concept of histogenetically different ampullary carcinomas which are developing from the intestinal or from the pancreaticobiliary type mucosa of Vater's papilla. Molecular alterations in ampullary carcinomas are similar to those of colorectal as well as pancreatic carcinomas, although they appear in different frequencies. In future studies molecular alterations in ampullary carcinomas should be correlated closely with the different histologic tumor types. The histologic classification should reflect consequently the histogenesis of ampullary tumors from the two different types of papillary mucosa.