The pathogenesis of a choledochal cyst remains uncertain. One possible cause is that the junction of the common bile duct and the pancreatic duct before their entry into the sphincter of Oddi may allow reflux of pancreatic enzymes into the common bile duct, causing inflammation, localized weakness, and dilatation of the duct. Other possibilities are that they represent malformations of the common duct or they occur as part of a broad disease spectrum that includes neonatal hepatitis and biliary atresia.
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