ETS proto-oncogene 1, transcription factor (ETS1) is involved in various immune responses. Genome-wide association studies on systemic lupus erythematosus in Chinese populations identified the association of ETS1 polymorphism in 3′ untranslated region, rs1128334A, which was associated with lower ETS1 expression. In view of substantial sharing of susceptibility genes across multiple autoimmune diseases, we examined whether ETS1 is associated with a rare autoimmune rheumatic disease, anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV). Association of rs1128334 was tested in 466 Japanese patients with AAV and 1099 healthy controls by logistic regression analysis under the additive model. AAV patients were classified into 285 microscopic polyangiitis (MPA), 92 granulomatosis with polyangiitis (GPA), 56 eosinophilic GPA, and 33 unclassifiable AAV, according to the European Medicines Agency (EMEA) algorithm. Among the patients, 376 were positive for MPO–ANCA and 62 for PR3–ANCA. When the patients were classified according to the EMEA classification, rs1128334A allele was significantly increased in GPA (P = 0.0060, Pc = 0.030, odds ratio (OR), 1.54; 95% confidence interval (CI), 1.13–2.10). With respect to the ANCA specificity, significant association was observed in PR3–ANCA positive AAV (P = 0.0042, Pc = 0.021, OR, 1.72; 95% CI, 1.19–2.49). In conclusion, ETS1 polymorphism was suggested to be associated with GPA and PR3–ANCA positive AAV in a Japanese population.