Antineutrophil cytoplasmic antibodes (ANCA) are markers of necrotizing vasculitis. ANCA have been recently detected in the two forms of inflammatory bowel disease (IBD), ulcerative colitis (UC) and Crohn's disease (CD). To assess the possible role of ANCA in the diagnosis and management of IBD we studied the prevalence of ANCA at diagnosis and during follow-up in a group of 89 IBD patients. The relationship between ANCA and clinical features of IBD was investigated. ANCA assayed by indirect immunofluorescence were detected in 38/52 (73%) of the UC patients but only 6/37 (16.6%) of the CD patients (P<0.005) and in none of the controls. In the UC group, but not in the CD group, there was a positive correlation between ANCA and disease activity. The sensitivity and specificity of ANCA for the diagnosis of UC were 73 and 83.7% respectively. The most commonly observed pattern of ANCA in IBD patients was perinuclear: in 84% of the UC and 66.6% of the CD patients positive for ANCA, respectively. However, careful comparison of IFL patterns revealed some distinct features of IBD-associated ANCA when compared to vasculitis-associated ANCA. In addition, most ANCA positive sera from IBD patients were negative for antibodies to proteinase 3 and myeloperoxidase by ELISA. These results suggest that the autoantigens recognized by ANCA are different in patients with IBD from those with necrotising vasculitis.