Antineutrophil cytoplasmic antibodies (ANCA) have been identified in the serum of 50-80% of ulcerative colitis (UC) patients. UC-associated ANCA yield a perinuclear staining pattern (pANCA) with alcohol-fixed neutrophils. More recently, pANCA have been detected in the serum of patients with primary sclerosing cholangitis (PSC) and other autoimmune liver diseases. Up to 70% of PSC patient sera and up to 92% of sera from patients with well-defined type 1 autoimmune hepatitis (type 1 AIH) were found to express pANCA. Such expression by patients with PSC and type 1 AIH raises questions concerning the relationship of these pANCA to each other and to that of UC. Differences and similarities in pANCA characteristics are found among the three diseases, suggesting the use of pANCA to define specific disease subgroups. Our recent finding that the UC-associated pANCA reactive antigen was localized within the nuclear domain prompted an examination of whether DNase treatment of neutrophils would alter antigenic recognition by the pANCA of UC, PSC, and type 1 AIH. While loss of antigenic recognition after DNase digestion of neutrophils was a dominant feature of the UC-associated pANCA, the majority of PSC and type 1 AIH pANCA recognized cytoplasmic constituents. These results further support the feasibility of defining and/or distinguishing disease subgroups based on the characterization of respective pANCA.