Considerable variability has been reported in the frequency and specificity of anti-neutrophil cytoplasmic antibody with a perinuclear staining pattern (pANCA) in patients with chronic liver disease, especially in primary sclerosing cholangitis (PSC), and in inflammatory bowel disease. This study examines the presence of pANCA in patients with these disorders, in particular those with PSC complicated by other biliary disease, and also patients who had undergone orthotopic liver transplantation. An indirect immunofluorescent technique was used to measure pANCA with serum diluted 1 : 20. Ten of 39 (26%) patients with PSC had detectable pANCA, as did two of nine (22%) with autoimmune chronic active hepatitis (AICAH) but none of the 51 patients with other forms of chronic liver disease. The presence of pANCA was significantly more frequent in patients who had PSC with biliary tract complications, in particular calculi (seven of 16 with vs three of 23 without; P = 0.03). Eight of the 12 pANCA-positive patients with PSC or AICAH had undergone hepatic transplantation. This was more likely than in patients with PSC or AICAH who were pANCA negative (10 of 36; P = 0.02). To date, pANCA has been detected after transplantation in four patients with PSC and one with AICAH, In patients with PSC or AICAH, pANCA should be sought as a marker of prognosis.