OBJECTIVE To compare the disease spectrum of consecutive patients with antineutrophil cytoplasmic autoantibodies directed against proteinase 3 (anti-PR3) or myeloperoxidase (anti-MPO). METHODS Retrospective analysis. METHODS Three teaching hospitals in the Netherlands. METHODS Clinical features at presentation, histopathological characteristics and outcome. METHODS All consecutive patients who tested positive for anti-PR3 (n=46) or anti-MPO (n=46) over an 8-year-period. RESULTS At diagnosis, patients with anti-PR3 had a higher vasculitis activity index than patients with anti-MPO (P < 0.001). The mean (SD) number of affected organs in the anti-PR3 group exceeded that of the anti-MPO group (3.9 (1.4) and 2.2 (1.1), respectively; P < 0.01). The combination of renal and respiratory tract involvement was present in as many as 78.3% of patients with anti-PR3 and in only 23.9% of patients with anti-MPO (P < 0.01). Renal-limited disease exclusively occurred in patients with anti-MPO. Granulomas were found in 41.3% of anti-PR3- but in only 4.3% of anti-MPO-positive patients (P < 0.01). All anti-PR3-positive patients had Wegener's granulomatosis or microscopic polyangiitis. By contrast, diagnoses in the anti-MPO group were more diverse: idiopathic necrotizing crescentic glomerulonephritis (26.1%), microscopic polyangiitis (26.1%). Churg-Strauss syndrome (4.3%), Wegener's granulomatosis (2.2%), giant cell arteritis (2.2%), clinically suspected vasculitis (19.6%), as well as miscellaneous nonvasculitic disorders (19.6%). During follow-up, 10 anti-PR3-positive patients had 11 relapses whereas only 3 patients with anti-MPO relapsed (P=0.04). CONCLUSIONS A large divergence was seen in the disease spectrum between patients with anti-PR3 and those with anti-MPO. In particular, extra-renal disease manifestations, granuloma formation and relapses were more prominent in anti-PR3- than in anti-MPO-positive patients.