The immunopathogenic importance of neutrophil cytoplasmic autoantibodies in ulcerative colitis and primary sclerosing cholangitis is unknown. These autoantibodies were investigated before and after liver transplantation in 9 patients with primary sclerosing cholangitis. Sera from 10 patients transplanted for metabolic disorders or hemangioma served as controls. Before liver transplantation neutrophil cytoplasmic autoantibodies, producing a perinuclear pattern by indirect immunofluorescence on ethanol fixed neutrophils, were present in all patients with primary sclerosing cholangitis. A decline in titer was noted in the first months after liver transplantation. During long-term follow up, the autoantibodies remained present and most often the titer did not differ from before transplantation. They were not directed against proteinase 3, myeloperoxidase, elastase or lactoferrin. All but one of the control patients were negative for the autoantibody. No relation was seen, before or after transplantation, with ulcerative colitis or proctocolectomy. There was no recurrence of primary sclerosing cholangitis in any of the patients as judged by liver histology. We conclude that neutrophil cytoplasmic autoantibodies remain present after liver transplantation for primary sclerosing cholangitis and that its synthesis is not related to the presence of the diseased organ(s). The primary disease process in primary sclerosing cholangitis and ulcerative colitis may well be a disturbance of the immune system.