Objective The vasculitis diseases granulomatosis with polyangiitis (GPA), microscopic polyangitis (MPA) and eosinophilic granulomatosis with polyangitis (EGPA) consist of anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitides (AAV). As the major susceptibility genes were identified in Europeans, and the non-ignorable population heterogeneity and race difference, We investigated the linkage between putative AAV-related genes (HLA-DPB1, CD226 and PRTN3) and AAV in a Han Chinese population. Methods A Sequenom MassArray system was used to genotype single nucleotide polymorphisms (SNPs) in 196 Han Chinese patients with AAV (100 with GPA, 76 with MPA, 20 with EGPA) and 485 ethnically-matched healthy controls. Results The frequency of the rs3117242 variant T allele was significantly higher in GPA patients than in the controls (68.0% compared with 50.4%, OR = 2.09, 95% CI: 1.51-2.88, Bonferroni corrected P-value [Pc] ＜0.001), but was not significantly different between MPA patients and controls (Pc = 0.09，Pc = 0.94). The same results were obtained via genotype distribution. The allele and genotype distributions of the other polymorphisms were not significantly associated with AAV patients as a whole or with GPA or MPA or EGPA patients considered separately. Conclusion The rs3117242 of HLA-DPB1 could be considered a genetic risk factor for GPA in Chinese Han people. These findings provide further insights and clues in the etiology of GPA