Background: Disease relapse remains a major problem in the management of antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV). In European populations, HLA-DPB1*04:01 is associated with both susceptibility and relapse risk in proteinase 3-ANCA positive AAV. In a Japanese population, we previously reported an association between HLA-DRB1*09:01 and DQB1*03:03 with susceptibility to, and DRB1*13:02 with protection from, myeloperoxidase-ANCA positive AAV (MPO-AAV). Subsequently, the association of DQA1*03:02 , which is in strong linkage disequilibrium with DRB1*09:01 and DQB1*03:03 , with MPO-AAV susceptibility was reported in a Chinese population. However, an association between these alleles and risk of relapse has not yet been reported. Here, we examined whether HLA-class II is associated with the risk of relapse in MPO-AAV., Methods: First, the association of HLA-DQA1*03:02 with susceptibility to MPO-AAV and microscopic polyangiitis (MPA) and its relationship with previously reported DRB1*09:01 and DQB1*03:03 were examined in 440 Japanese patients and 779 healthy controls. Next, the association with risk of relapse was analyzed in 199 MPO-ANCA positive, PR3-ANCA negative patients enrolled in previously reported cohort studies on remission induction therapy. Uncorrected P values (P uncorr ) were corrected for multiple comparisons in each analysis using the false discovery rate method., Results: The association of DQA1*03:02 with susceptibility to MPO-AAV and MPA was confirmed in a Japanese population (MPO-AAV: P uncorr =5.8x10 -7 , odds ratio [OR] 1.74, 95% confidence interval [CI] 1.40-2.16, MPA: P uncorr =1.1x10 -5 , OR 1.71, 95%CI 1.34-2.17). DQA1*03:02 was in strong linkage disequilibrium with DRB1*09:01 and DQB1*03:03 , and the causal allele could not be determined using conditional logistic regression analysis. Relapse-free survival was shorter with nominal significance in carriers of DRB1*09:01 (P uncorr =0.049, Q=0.42, hazard ratio [HR]:1.87), DQA1*03:02 (P uncorr =0.020, Q=0.22, HR:2.11) and DQB1*03:03 (P uncorr =0.043, Q=0.48, HR:1.91) than in non-carriers in the log-rank test. Conversely, serine carriers at position 13 of HLA-DRβ1 (HLA-DRβ1_13S), including DRB1*13:02 carriers, showed longer relapse-free survival with nominal significance (P uncorr =0.010, Q=0.42, HR:0.31). By combining DQA1*03:02 and HLA-DRβ1_13S, a significant difference was detected between groups with the highest and lowest risk for relapse (P uncorr =0.0055, Q=0.033, HR:4.02)., Conclusion: HLA-class II is associated not only with susceptibility to MPO-AAV but also with risk of relapse in the Japanese population., Competing Interests: AK has received research grants from Ichiro Kanehara Foundation, Takeda Science Foundation, and Japan College of Rheumatology, and honoraria for lectures from Chugai Pharmaceutical Co. Ltd. K-ES has received a research grant from Pfizer Inc., and honoraria for lectures from Glaxo SmithKline K.K. FH has received honoraria for lectures from Janssen Pharmaceuticals, Ono Pharmaceuticals, and Mitsubishi Tanabe Pharma. SK has received honoraria for the lectures from Novartis Pharma K.K, Eli Lilly Japan K.K., Chugai Pharma, Asahi Kasei Pharma, Gilead Sciences and Janssen Pharma K.K. KN has received speaking fee from Chugai Pharmaceutical Co. Ltd. TS has received grants from AsahiKASEI Co., Ltd., Daiichi Sankyo, Chugai Pharmaceutical Co. and Ono Pharmaceutical, consulting fees from AsahiKASEI Co., Ltd., and honoraria for the lectures from Abbvie Japan Co., Ltd. AsahiKASEI Co., Ltd. Astellas Pharma Inc., Ayumi Pharmaceutical, Bristol Myers Squibb K.K., Chugai Pharmaceutical Co., Ltd, Eli Lilly Japan K.K., Mitsubishi-Tanabe Pharma Co., Ono Pharmaceutical, Pfizer Japan Inc., Takeda Pharmaceutical Co. Ltd., and UCB Japan Co. Ltd. NTa has received grants from Astellas, Ayumi, Asahi Kasei Pharma, Asahi Kasei Medical, AbbVie, Eisai, Nippon Boehringer Ingelheim, Novartis Pharma, Bayer Yakuhin, Tanabe Mitsubishi, Taisho, and Chugai. NTa has received speaker fees and/or consulting fees from AbbVie, Eli Lilly Japan, Eisai, GlaxoSmithKline, Novartis, Bristol Myers Squibb, TanabeMitsubishi, Chugai and Janssen. KI and YK have received grants from Asahi Kasei Pharma, Eizai, Teijin Pharma, and Chugai Pharmaceutical. KI has received honoraria for lectures from Asahi Kasei Pharma and Abbvie. HM has served on advisory boards for Boehringer Ingelheim and Travere Therapeutics. MH has received grants from AbbVie Japan GK, Boehringer Ingelheim Japan, Inc., Bristol Myers Squibb Co., Ltd., Chugai Pharmaceutical Co., Kissei Pharmaceutical Co., Ltd., Mitsubishi Tanabe Pharma Co., and Teijin Pharma Ltd. MH has received consulting fee from Kissei Pharmaceutical Co., Ltd., honoraria for lectures from AbbVie Japan GK, Boehringer Ingelheim Japan, Inc., Bristol Myers Squibb Co., Ltd., Chugai Pharmaceutical Co., Kissei Pharmaceutical Co., Ltd. Mitsubishi Tanabe Pharma Co., and Teijin Pharma Ltd., participation for Advisory Board for Kissei Pharmaceutical Co., Ltd. NTs has received grants from Bristol-Myers Squibb K.K., the Naito Foundation, the Uehara Memorial Foundation, and collaborative research fund from H.U. Group Research Institute G.K. NTs has received award grants from Japan College of Rheumatology and Japan Rheumatism Foundation, and honoraria for lectures from Teijin Ltd. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Kawasaki, Sada, Kusumawati, Hirano, Kobayashi, Nagasaka, Sugihara, Ono, Fujimoto, Kusaoi, Tamura, Kusanagi, Itoh, Sumida, Yamagata, Hashimoto, Makino, Arimura, Harigai and Tsuchiya.)