Wegener's Granulomatosis (WG) is closely associated with antineutrophil cytoplasmic autoantibodies (ANCA), particularly those directed to proteinase 3 (PR3). ANCA directed to myeloperoxidase (MPO) are associated with microscopic polyangiitis (MPA) and the Churg Strauss syndrome. PR3-ANCA associated vasculitis differs from MPO-ANCA associated vasculitis particularly in the occurrence of granulomatous inflammation and more widespread disease in the former condition. Studies in experimental animals strongly suggest a pathogenic role for MPO-ANCA, but this is less clear for PR3-ANCA. Here, we review pathogenic pathways in PR3-ANCA associated vasculitis focussing on unique patterns of PR3 expression on the neutrophil membrane in WG, as surface expression of PR3 is a prerequisite for stimulation by PR3-ANCA; (PR3-specific) cellular immunity in WG; and the role of Staphylococcus aureus carriage in this disease. These factors, together, may explain, at least in part, differences in clinical expression between MPO-ANCA and PR3-ANCA associated vasculitis.