This study evaluated the performance of 12 assays for antineutrophil cytoplasmic antibodies (ANCA) directed against proteinase 3 (PR3) and myeloperoxidase (MPO) in 55 active and 68 treated cases of vasculitis and in nonvasculitic disease. It examined within- and between-assay precision; binding curves, binding levels, and interassay consistency; and sensitivity, specificity, and receiver operating characteristic analysis. All assays were highly sensitive for active vasculitis (median, 94%; range, 91%-96%), but sensitivities were more varied in treated disease (median, 69%; range, 57%-82%). Binding curves and binding levels were also very variable in PR3-ANCA and MPO-ANCA assays. This has implications for studies correlating ANCA levels with disease activity and in developing ANCA-based treatment guidelines. PR3-ANCA and MPO-ANCA assays need to be standardized as a matter of urgency, but in the meantime, individual laboratories must understand the limitations of the assays used, especially with low-level ANCA in treated vasculitis and nonvasculitic disease.