Primary Sjögren’s syndrome is one of the most common autoimmune diseases. To identify novel genetic susceptibility loci for primary Sjögren’s syndrome, we performed a three-stage genome-wide association study (GWAS) in Han Chinese. At the discovery stage, 556,134 autosomal SNPs were analyzed in 542 cases and 1,050 controls. Promising associations were validated in two-stage replications with 1,303 cases and 2,727 controls. The combined analysis identified a new susceptibility locus for primary Sjögren’s syndrome. Our analysis also confirmed previously reported primary Sjögren’s syndrome associations in Europeans in several loci. Fine mapping of the region around the new locus confirmed the association and further extended the region of the new locus.