The embryogenesis of pancreaticobiliary maljunction is inferred from the embryogenesis of duodenal atresia. The epithelial cells of the duodenum begin to proliferate and completely plug the lumen, but a process of vacuolation recanalizes the duodenum. Recanalization of the common duct frequently appears with two lumina and openings into the duodenum with two orifices. These two major canals create a narrow segment of the duodenum and this narrow zone is the area in the duodenum that is most prone to faulty recanalization and atresia formation. A bifid biliary system inserts at blind upper and lower pouches of the duodenum, and the common bile duct inserts in a Y fashion. The common bile duct inserts at the stenotic segment, and the end result is a T-shaped formation in patients with duodenal stenosis. During the development of the bile duct, abnormal fusion may occur between the bile duct and branches of the right ventral pancreatic duct. The site in the bile duct where a branch of the pancreatic duct joins is likely to develop atresia due to disturbance of the recanalization process, as seen in duodenal atresia. Severe impairment of vacuolation causes divided atretic bile duct at the site where the pancreatic duct inserts in a Y-fashion into the upper and lower bile duct. Moderate impairment of vacuolation causes a stenosis at the site where the pancreatic duct inserts in a T-shape, with a moderate dilatation of the bile duct.