Sclerosing cholangitis with autoimmune pancreatitis (SC with AIP) takes a better clinical course than primary sclerosing cholangitis due to the effectiveness of steroid therapy. However, the morphological and functional changes in SC with AIP during long-term observation have not yet been reported. We encountered two cases of SC with AIP that resulted in liver atrophy and portal obstruction during long-term observation. One case was followed up without steroid therapy. The other case was treated with endoscopic biliary drainage initially. These cases may provide further information regarding steroid therapy for SC with AIP.