To test the hypothesis that anti-neutrophil cytoplasm autoantibodies (ANCAs) interfere with the functions of proteinase 3 (PR3) (the Wegener autoantigen) and alpha 1-antitrypsin (alpha 1AT), complexes of PR3/alpha 1 AT and PR3/PR3-ANCA-IgG were assayed Plasma samples were obtained from 44 patients with Wegener's granulomatosis (WG): 34 had active disease (88% ANCA positive) whereas 10 patients were in remission (20% ANCA positive). Plasma samples from 14 of the patients with active disease were also available at the time of remission. The complexes of PR3/alpha 1 AT and PR3/PR3-ANCA-IgG were detected by capture enzyme-linked immunoassays (ELISAs) alpha 1 AT deficiency was evaluated by determining PiZ alleles by ELISA. Eight (18%) of the patients were PiZ positive. The frequency of this alpha 1-antitrypsin phenotype in the Scandinavian population is 4.7% (P < 0.001). The median PR3/alpha 1AT complex level in the PiZ-positive group with active disease (n = 5) was similar to the level in the PiZ-negative group with active disease. During remission the median level for the PR3/alpha 1AT complex was significantly higher than in the acute group (P < 0.001) including both PiZ-positive and PiZ-negative patients. No difference between PiZ positivity and PiZ negativity could be found in the remission group. PR3/PR3-ANCA-IgG complexes were found in patients with acute disease as well as in patients in remission, in almost equal frequency. This complex was also present in 13/18 ANCA-negative samples from patients in remission. Finally, purified IgG fractions from WG patients were examined for their capacity to inhibit binding between PR3 and alpha 1AT. An effect on the binding between PR3 and alpha 1AT by PR3-ANCA could not be demonstrated. Thus, our results do not support the hypothesis that PR3-ANCA interferes with the binding between PR3 and alpha 1AT. However, the high prevalence of the PiZ alleles among WG patients suggests that an imbalance between proteinases and alpha 1AT may be of importance in this disease. The clinical usefulness of both the PR3/alpha 1AT and the PR3/PR3-ANCA-IgG complexes and the possible influence on ANCA detection need to be examined in prospective longitudinal studies.