The first genome-wide association study (GWAS) of IgG4-related disease, involving 857 Japanese patients with IgG4-related disease and 2,082 healthy participants, has identified two susceptibility loci: HLA-DRB1 and FCGR2B. The strongest disease association in HLA-DRB1 corresponded to an amino acid residue in the peptide-binding groove of HLA-DRB1. The single nucleotide variant in FCGR2B (rs1340976) was associated with increased expression of FCGR2B, as well as with specific clinical features of IgG4-related disease (including the number of swollen organs and IgG4 concentration at diagnosis).