BACKGROUND: Although there are two peaks in the age distribution of primary sclerosing cholangitis (PSC) in Japan, the clinical differences between the patients with an older or younger onset age have not been reported. METHODS: We compared clinical features of 18 patients with onset age less than 50 years (younger group) and ten PSC patients with onset age above 50 years (older group). RESULTS: An association with ulcerative colitis (UC) was recognized in six patients in the younger group and in one in the older group. High serum IgE (>170 IU/ml) was observed more frequently in the older than in the younger group (1/10 vs. 7/8, P = 0.0029). Mean serum IgM tended to be higher in the younger group (198 vs. 119 mg/dl, P = 0.083). More patients received liver transplantation or continuous bile drainage, or developed liver failure or cholangiocellular carcinoma in the younger than in the older group (11/18 vs. 1/10, P = 0.016). CONCLUSIONS: Older PSC patients have higher IgE, possibly less association with UC, lower IgM, and a better prognosis. The pathogenesis of PSC may be different between older and younger patients.