The outcomes of primary sclerosing cholangitis (PSC) after living donor liver transplantation (LDLT) in a large series have not been reported. We aimed to determine long-term patient and graft survival, risk factors for PSC recurrence, and the significance of recurrence after LDLT in a Japanese registry. Questionnaires concerning patient characteristics, treatments, and clinical courses were used. Data of 114 patients undergoing primary LDLT for PSC from July 1996 to December 2008 in 29 institutions were evaluated. For strict diagnoses of recurrence, patients with hepatic artery thrombosis (n = 8), ABO-blood-type-incompatible transplantation (n = 8), and established ductopenic rejection (n = 2) were excluded and 96 patients were analyzed for risk factors. Recurrence was diagnosed in 26 patients (27%) at 8 to 79 months after transplantation. Patient, graft, and recurrence-free survivals were 78, 74 and 57% at 5 years after LDLT, respectively. The graft loss rate was 69 versus 23% in patients with versus without recurrence, respectively. Multivariate analysis revealed that high MELD scores, first-degree-relative donors, postoperative CMV infection, and early biliary anastomotic complications were significant risk factors for recurrence. PSC recurrence was a significant risk factor of graft loss but not patient death. PSC recurrence was frequent and had significant impacts on outcomes after LDLT.