Two cases with an anomalous arrangement of the pancreaticobiliary ducts (APBD) are reported in order to investigate the mechanism of carcinogenesis of the extrahepatic biliary tract from the aspect of DNA ploidy analysis. Highly elevated biliary enzymes were found in both cases. Although inflammatory changes without any metaplasia or neoplasia were observed histologically, a cytofluorometric nuclear DNA ploidy analysis showed an aneuploid low ploidy pattern in a histogram of the gall bladder, an aneuploid high ploidy pattern in a histogram of the common bile duct in one patient, and a diploidy pattern in the gall bladder, an aneuploid low pattern in the common bile duct in another case. These results may show that APBD may play a role in the development in DNA ploidy abnormality with refluxed pancreatic juice which may induce repeated irritation and inflammation. Radical surgery including a complete excision of the extrahepatic biliary tract followed by reconstruction may achieve better results with regard to undesirable consequences with an abnormal nuclear DNA ploidy pattern and decrease the likelihood of developing carcinoma.