Most laboratories screen for antineutrophil cytoplasmic antibodies (ANCA) with indirect immunofluorescence (IIF) and confirm cytoplasmic (C-ANCA) and perinuclear (P-ANCA) staining with ELISAs for proteinase 3 (PR3) and myeloperoxidase (MPO) specificities. This study determined the concordance of ANCA test results from 48 diagnostic laboratories participating in a national Quality Assurance programme, that used different assays and methods and varied in expertise. Laboratories were circulated with a questionnaire about their techniques, and provided with 24 sera for testing over a 30 month period. Results for individual sera were compared with the 'observed consensus' found in more than 50% of laboratories. The 23 laboratories (48%) that responded to the questionnaire used 5 different IIF substrates and 11 ELISAs, and differed in other aspects of testing. Concordance for ANCA test results was greater for IIF-positive (n=22, median 96%, range 68%-100%) than an IIF-negative serum (median 64%); for C-ANCA (n=8, median 89%, range 66-100%) rather than P-ANCA (n=10, median 76%, range 52-88%); for MPO-ANCA (n=5, median 100%) rather than PR3-ANCA (n=7, median 89%, range 82-100%); and for strongly-positive (n=2, median 97%, range 96-97%) rather than low positive PR3-ANCA (n=4, median 80%, range 74-86%). Concordance for test results might be improved with further standardisation of testing methodologies.