A 55-yr-old female was hospitalized with epigastric pain. Conventional ultrasonography revealed marked dilation of the common bile duct (CBD). Endoscopic retrograde cholangiopancreatography showed fusiform dilation of the CBD. The common channel of the pancreatic duct and choledochus was 20 mm long. A diagnosis of congenital choledochal dilation accompanied by anomalous arrangement of the pancreaticobiliary ductal system (AAPBDS) was made. Intraductal ultrasonography (IDUS) was performed. IDUS demonstrated the union of the pancreatic duct and choledochus within the pancreatic parenchyma. This meant that the union existed outside the duodenal wall, confirming the diagnosis of AAPBDS. Although endoscopic retrograde cholangiopancreatography alone could show the maljunction in this case, simultaneous IDUS will be useful in making an accurate diagnosis of AAPBDS.