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Autoimmune pancreatitis (AIP) is a recently proposed disease entity, in which an elevated serum IgG4 is characteristic. This disease is sometimes associated with other inflammatory diseases: Sjögren's disease, or sclerosing cholangitis. The aim of the present paper was to examine the difference in pathophysiology between AIP-associated sclerosing cholangitis (AIP-SC) and primary sclerosing cholangitis (PSC). The clinicopathological findings and the immunohistochemical expressions of IgG subclasses (IgG1, IgG2, IgG3, and IgG4) were evaluated for the two aforementioned diseases (six patients with each disease). Radiologically, the extrahepatic bile duct was involved in AIP-SC, whereas both extrahepatic and intrahepatic bile ducts were involved in PSC. Clinically, bile duct lesions in the former responded well to steroid therapy. Histologically, various degrees of mononuclear cell infiltration and fibrosis around bile ducts and portal tracts were found in all patients. Immunohistochemically, the IgG4-positive plasma cell/mononuclear cell ratio was significantly higher in AIP-SC than in PSC (P < 0.05). The IgG4-positive plasma cell/mononuclear cell ratio is a useful index to help distinguish AIP-SC from PSC. A mechanism similar to that involved in AIP may be involved in AIP-SC. The latter is a distinct clinicopathological entity that should be distinguished from PSC because it responds well to steroid therapy.