Antineutrophil cytoplasmic antibodies (ANCA) are widely used as a useful diagnostic marker for small vessel vasculitides, although the test may occasionally be positive in various other conditions. The aim of this study was to assess ANCA in various clinical-pathological settings. ANCA were tested by indirect immunofluorescence and enzyme-linked immunosorbent assay and were found to be positive in 423 patients in the period from 1989-1999. Patients were grouped in accordance with their clinical-pathological setting as follows: 1. pauci-immune vasculitis confirmed by biopsy (n = 151), 2. clinically suspected vasculitis (n = 59), 3. inflammatory bowel diseases and autoimmune hepato-biliary disorders (n = 83), and 4. miscellaneous diseases (n = 130). The association of proteinase 3 ANCA with Wegener's granulomatosis (45/56) and myeloperoxidase ANCA with microscopic polyangiltis (45/54) and pauci-immune necrotising glomerulonephritis (24/28) was established. However, ANCA with other specificities were also shown to be present in these forms of vasculitides. ANCA, specific mostly for myeloperoxidase but also for other or unknown ANCA antigens, frequently revealing atypical immunofluorescence patterns, were characteristically found in other diseases. The titres of ANCA were significantly higher (p < 0.05) in patients with pauci-immune vasculitis than in those with clinically suspected vasculitis and other diseases. In conclusion, well standardised techniques for ANCA testing in conjunction with the clinical picture and histopathologic findings, if available, may significantly contribute to the diagnosis of small vessel vasculitides.