Anomalous union between the pancreatic and biliary systems (APBDU) has been reported to produce choledochal cyst. The aim of this experiment was to evaluate the role of sphincteroplasty to adverse effect of APBDU in an animal model. Twelve mongrel puppies were randomly divided into a control group (n = 5) and an experimental group (n = 7). A well-established model of APBDU was produced in both groups. Transduodenal sphincteroplasty was performed only on the experimental group. For all animals, serial chemical analyses of serum were performed, and biliary tree sizes were measured by magnetic resonance cholangiography 2.5 months after the experimental surgery. At the time of animal sacrifice, 3 months after the experimental surgery, operative cholangiography was performed, and bile juice and tissues were obtained for chemical analysis and histologic examination. Dilatation of the bile duct and thickening of the wall of the bile duct were observed less frequently in the experimental group than in the control group. There were no significant differences found in pancreatic enzyme activity in the bile juice between the two groups. Denudation of the mucosa was the predominant mucosal change seen in the experimental group, while epithelial hyperplasia was the predominant mucosal change found in the control group. Our experiment shows that sphincteroplasty is not effective to prevent the pancreaticobiliary reflux, but may be effective to reduce the degree of both bile duct dilatation and mural thickening in the APBDU puppy model.