The present study examined the association between various human leukocyte antigens (HLA) and cytoplasmic-antineutrophil cytoplasmic antibody (cANCA)-positive Wegener's granulomatosis (WG) in Japanese subjects to determine whether HLA antigens are involved in the pathogenesis of this disease. The study involved 16 subjects with cANCA-positive WG treated in our department. HLA-typing of the lymphocytes was performed using a lymphocyte microcytotoxicity assay. Of the subjects with cANCA-positive WG, 62.5% (10/16) were positive for HLA-DR9, as compared to 26% of the healthy control subjects. This HLA-DR9 elevation was statistically significant (p < 0.01, Pc < 0.05); we also noted a weaker association between HLA-B55 and cANCA-positive WG (p < 0.05). The results indicate that an association may exist between certain HLA-class allotypes and WG.