The main pancreatic duct begins in the tail of the pancreas and runs through the parenchyma of the gland to the pancreatic head: here it turns inferiorly and is closely related to the bile duct. The main pancreatic duct and bile duct usually unite to form the short, dilated hepatopancreatic ampulla (of Vater), which opens into the descending part of the duodenum at the summit of the major duodenal papilla. At least 25% of the time, the ducts open into the duodenum separately.

The sphincter of the pancreatic duct (around the terminal part of the pancreatic duct), the sphincter of the bile duct (around the termination of the bile duct), and the hepatopancreatic sphincter (of Oddi) - around the hepatopancreatic ampulla - are smooth muscle sphincters that control the flow of bile and pancreatic juice into the ampulla and prevent reflux of duodenal content into the ampulla.

The accessory pancreatic duct opens into the duodenum at the summit of the minor duodenal papilla. Usually, the accessory duct communicates with the main pancreatic duct. In some cases, the main pancreatic duct is smaller than the accessory pancreatic duct and the two may not be connected. In such cases, the accessory duct carries most of the pancreatic juice.