Background and Aim: Autoimmune hepatitis/primary sclerosing cholangitis (PSC) overlap syndrome (AIH/PSC), PSC and sclerosing cholangitis with autoimmune pancreatitis (SC-AIP) are autoimmune diseases that can be diagnosed by endoscopic retrograde cholangiography (ERC), and this study was conducted to identify the clinicopathological differences between them. Methods: We retrospectively compared the clinical findings, ERC findings, and liver biopsy findings in 7 cases of AIH/PSC, 22 cases of PSC and 30 cases of SC-AIP. AIH was diagnosed as definite or probable based on the reports of the International Autoimmune Hepatitis group. Results: There were significant differences between the AIH/PSC group, PSC group, and SC-AIP group in the following parameters: mean age at the time of diagnosis (31.4 ± 20.8, 41.2 ± 17.8, and 66.7 ± 8.3 years, respectively, p < 0.01), serum AST level (400 ± 630, 71 ± 50, and 120 ± 160 IU/l, respectively, p < 0.05), serum γ-globulin level (2.9 ± 1.2, 1.5 ± 0.4, and 2.0 ± 0.6 g/dl, p < 0.001), and serum IgG4 level (25 ± 6, 39 ± 21,and 395 ± 260 mg/dl, p = 0.003). ERC revealed band-like strictures, beaded appearance, and pruned-tree appearance significantly more frequently in the AIH/PSC group and PSC group (p < 0.001), whereas segmental strictures and strictures of the distal third of the common bile duct were significantly more common in the SC-AIP group (p < 0.001). Liver biopsy revealed fibrous cholangitis significantly more frequently in the AIH/PSC group and PSC group, and interface hepatitis more frequently in the AIH/PSC group. No advanced fibrous change corresponding to Ludwig's stage 3 and 4 was observed in any of the SC-AIP specimens. IgG4-positive plasma cell infiltration of the liver was significantly more severe in SC-AIP than in AIH/PSC and PSC (p < 0.001). Treatment included ursodeoxycholic acid (UDCA) and prednisolone (PSL) in the AIH/PSC group, UDCA in the PSC group, and PSL in the SC-AIP group. Subsequent ERC showed no improvement in any of the AIH/PSC and PSC cases, but all SC-AIP patients responded to steroid therapy, and improvement in the strictures was observed. Liver failure developed in 75% (3/4) of the AIH/PSC patients and 50% (6/12) of the PSC patients over a 5-year course of treatment, however, none of the SC-AIP patients developed liver failure. Conclusions: Based on the differences between the patients' ages, blood chemistry findings, ERC findings, liver biopsy findings, and clinical course, it has been shown that there are differences in between the clinical characteristics of AIH/PSC, PSC and SC-AIP, and in the present study we identified clinicopathological differences that facilitate the differential diagnosis between them.