Two children with spontaneous perforation of a choledochal cyst were treated successfully. In one of the patients an operative cholangiogram demonstrated not only fusiform dilatation of the common bile duct but also an unusual long common channel between the junction of the common bile duct and pancreatic duct, and the papilla. The long common channel, namely an anomalous choledocho-pancreatic ductal junction, under which there were concentrated bile acids and refluxed pancreatic juice, was thought to lead to chronic inflammation of the bile duct, followed by choledochal cyst and/or perforation of the cyst.