Autoimmune pancreatitis (AIP) is frequently associated with sclerosing cholangitis (SC). SC with AIP has a cholangiographic appearance that is often confused with primary sclerosing cholangitis (PSC) but only the former responds well to corticosteroid therapy. Detailed study of cholangiographic findings allows discrimination of SC with AIP from PSC. Band-like strictures, a beaded or pruned-tree appearance, and diverticulum-like outpouching were significantly more frequently observed in cases of PSC. In contrast, segmental strictures, dilation after confluent stricture, and strictures of the lower common bile duct were significantly more common in SC with AIP. The other systemic extrapancreatic lesions associated with AIP found in the literature were Sjögren's syndrome, ulcerative colitis, retroperitoneal fibrosis, sialadenitis, thyroiditis, and idiopathic thrombocytopenic purpura. In a comparison of the clinical course and laboratory data of our cases, gamma-globulin, IgG, and IgG4 levels were significantly higher in patients with AIP with systemic extrapancreatic lesions than those without them. In our immunohistochemical study, marked infiltration of IgG4+ plasma cells was frequently observed in the pancreas, liver, bile duct, and salivary glands of the AIP patients examined. In contrast, the degree of infiltration of IgG4+ plasma cells around the bile duct in the portal areas and the extrahepatic bile duct with PSC was significantly lower than with AIP. These results also suggest that AIP is a disease state clearly different from PSC. In addition, the normal epithelia of the pancreatic ducts, bile ducts, gallbladder, and salivary gland ducts reacting with the patients' sera was detectable by the anti-IgG4 antibody. Therefore, AIP may also affect extrapancreatic organs, and the sera of AIP patients may contain an IgG4 autoantibody to various organs.