Carcinomas of the Vaterian system are rare and presumably arise from preexisting adenomas (adenoma-carcinoma-sequence). Usually, biopsies are obtained to confirm and specify endoscopic findings, but differentiating reactive atypia from dysplasia or dysplasia from invasive carcinoma can sometimes be difficult or even impossible on morphological criteria alone. In case of invasive carcinoma, furthermore, the precise classification of carcinoma subtypes needs to be established since the distinct subtypes differ significantly in terms of clinical outcome. The cell adhesion proteins CD24, P-cadherin and S100A4 were shown to be expressed in several carcinomas and in dysplastic epithelium but only rarely in normal mucosa. We therefore investigated their expression in 177 carcinoma, 114 adenoma and 152 normal mucosa specimens of the ampulla of Vater. Although the expression of the cell adhesion proteins did not differ between the carcinoma subtypes, marked differences between normal mucosa, adenoma and carcinoma samples were observed. All marker proteins were expressed in less than 7% of normal mucosa samples (S100A4 in only 1% of cases) and showed an increasing expression from adenoma to invasive carcinoma. Our findings suggest that P-cadherin and S100A4 are helpful in discriminating normal mucosa or reactive atypia from neoplastic lesions. CD24 and S100A4, furthermore, can assist in the differential diagnosis of dysplasia vs invasive carcinoma.