Anomalous pancreaticobiliary ductal junction (APBDJ) induces various pancreatobiliary diseases. Because of the high incidence of biliary tract carcinoma, excision of the gallbladder and choledochal cyst is now recognized to be the treatment of choice for patients with choledochal cyst. However, surgical strategy for patients with APBDJ without cyst is not well evaluated. Forty-five consecutive patients with APBDJ (33 with cyst, 12 without cyst) treated over a 20-years period were divided into two groups based on the presence or absence of choledochal cyst and associated pancreatobiliary diseases were examined to evaluate the surgical strategy for patients without cyst. Mean age of patients without cyst was older (p < 0.01) than that of patients with cyst. Female/male ratio was 1.0 in patients without cyst while it was 4.5 when cyst was present. Carcinoma of the gallbladder or bile duct was found in 12% and pancreatitis in 21% of patients with cyst, while 33% of patients without cyst had gallbladder carcinoma or pancreatitis. Chronic calcifying pancreatitis was present in 17% of patients without cyst but not in patients with cyst. We conclude that a significantly higher incidence of gallbladder carcinoma necessitates cholecystectomy in patients with APBDJ without choledochal cyst. Excision of the extrahepatic bile duct is recommended for these patients at an early stage of pancreatitis to prevent an irreversible pancreatic damage.