The term chronic cholangitis comprises a heterogeneous group of intra- and/or extrahepatic diseases that may either be bacterially caused or immunologically mediated. In this review, we will focus on the latter and present the clinicopathological and pathogenetic aspects of primary biliary cirrhosis (PBC) and primary sclerosing cholangitis (PSC). The histopathological criteria are defined and differential diagnosis is discussed. Particular emphasis is given to overlap syndromes of PBC and PSC with autoimmune hepatitis. Finally, a diagnostic algorithm is presented.