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Antineutrophil cytoplasmic antibodies (ANCA) have been reported in up to 87% of patients with primary sclerosing cholangitis with or without ulcerative colitis (PSC +/- UC) and in 68% of those with UC only. Compared with other liver and diarrhoeal diseases, ANCA have high specificity for PSC (+/- UC) and UC only. This study aimed to determine the prevalence and significance of ANCA in these two diseases and whether the ANCA titre or IgG subclass, or both, could distinguish between PSC + UC and UC only. Subjects included 63 patients with PSC, 85 with UC, 17 with coeliac disease, and 10 with dermatitis herpeteformis and 36 normal subjects. ANCA was detected using the immunoalkaline phosphatase method. The IgG subclass of ANCA was determined in 27 PSC + UC and 30 UC only patients using a panel of mouse monoclonal antibodies specific for the IgG subclasses. At a serum dilution of 1:5, ANCA had a diagnostic sensitivity of 65% for all PSC and 45% for UC only. For PSC + UC the sensitivity was 70% at 1:5 (p = 0.004 v UC only). At 1:50, the sensitivity values were 54% and 25% respectively for PSC + UC and UC only (p = 0.0006). In PSC, ANCA positivity was significantly associated with extensive involvement of the biliary tree but not with other clinical parameters. In UC only, the median disease duration was significantly greater in ANCA positive patients. The PSC + UC ANCA showed increased IgG3 compared with UC only ANCA (p < 0.05), together with increased IgG2 and IgG4 (p = NS). ANCA is a diagnostic marker in PSC and UC. While the higher titres and different IgG subclass distribution of ANCA in PSC + UC patients compared with those with UC only may reflect differences in underlying immune regulation, determination of the ANCA titre and IgG subclass is unlikely to have a role in distinguishing between PSC + UC and UC only ANCA. Future identification of the antigen(s) for ANCA should allow the development of a more sensitive and specific test for the diagnosis of these two conditions and also determine if ANCA is associated with UC or PSC.