The sphincter of Oddi is located at the distal end of the pancreatic and bile ducts and regulates the outflow of bile and pancreatic juice. A common channel can be so long that the junction of the pancreatic and bile ducts is located outside of the duodenal wall, as occurs in pancreaticobiliary maljunction; in such cases, the action of the sphincter does not functionally affect the junction. Thus, biliopancreatic and pancreatobiliary refluxes occur, resulting in various pathological conditions in the biliary tract and in the pancreas. Biliopancreatic reflux could be confirmed by operative or postoperative T tube cholangiography, computed tomography combined with drip infusion cholangiography, histological detection of gallbladder cancer cells in the main pancreatic duct, and reflux of bile on the cut surface of the pancreas. Pancreatobiliary reflux could be diagnosed on the basis of an elevated amylase level in the bile, secretin-stimulated dynamic magnetic resonance cholangiopancreatography, and pancreatography via the minor duodenal papilla. Recently, it has become obvious that these refluxes can occur in individuals without pancreaticobiliary maljunction. Biliopancreatic reflux is related to the occurrence of acute pancreatitis, and pancreatobiliary reflux might be related to biliary carcinogenesis even in some individuals without pancreaticobiliary maljunction. Since few systemic studies exists with respect to diagnostic imaging techniques and clinical relevance of these refluxes in individuals with a normal pancreaticobiliary junction, further prospective clinical studies including appropriate management should be performed.