Wegener's granulomatosis is a systemic disease characterized by the presence of antineutrophil cytoplasm autoantibodies specific for proteinase 3 (PR3-ANCA). The functional characteristics of PR3-ANCA differ between quiescent and active disease, suggesting changes in the properties of the autoantibodies in time. Using biosensor technology, we found that PR3-ANCA of different patients (n = 8) recognize a limited number of overlapping regions on PR3 at the time of diagnosis of Wegener's granulomatosis. This area might cover an immunodominant epitope, common for PR3-ANCA from all patients, irrespective of the size of the total area recognized by an individual autoantibody. Experiments with sera (n = 4) collected at the moment of diagnosis and at the time of relapse showed that the individual epitope specificities of PR3-ANCA change during the course of the disease. These changes in epitope specificity of PR3-ANCA may be responsible for the differences in functional properties of these autoantibodies between various stages of the disease.