Cancer of the ampulla of Vater is an uncommon disease that leads to death in 60% of affected patients. There is general agreement that local spread of the tumour (T stage) is the only significant and independent prognostic factor for this cancer. Although the genetic mechanisms underlying the development of ampullary tumors are still mostly unknown because of their rarity, the genetic anomalies involved in tumor development might serve as additional prognostic markers. Cytogenetic studies may be helpful in identifying specific chromosome regions involved in these cancers. We studied two cases of poorly differentiated ampullary adenocarcinomas using conventional and molecular cytogenetics on direct preparations. The cytogenetic analysis revealed complex chromosome complements in both cases with different cell lines, rearrangements, chromosome markers, and aneuploidies. Interestingly, the involvement of the 1p36 region was a feature of both cases. The molecular studies showed an absence of high microsatellite instability (MSI) and the morphologic and immunohistochemical pattern did not suggest MSI. This study may help to characterized ampullary adenocarcinomas showing complex karyotypes, poor differentiation and poor prognosis. In these tumors, the 1p36 region may play a relevant role in the progression towards a high grade of anaplasia.