Zhang QY, Liu W, Li L, et al. - As Hashimoto’s thyroiditis (HT) and Graves’ disease (GD), the two main autoimmune thyroid diseases, have both similarities and differences, researchers here sought for the genetic basis that may aid in distinguishing HT from GD and provide better understanding of the differences between these two closely related diseases. In the current study, they selected 18 SNPs from 18 established GD risk loci and then genotyped these in 2,682 patients with HT, 4,980 patients with GD and 3,892 controls. In the Chinese Han population, 11 susceptibility loci for HT were recognized, with four loci including the rs1265883 in SLAMF6 locus, rs1024161 in CTLA4, rs1521 in MHC–IB region and rs5912838 in GPR174/ ITM2A at X chromosome, reaching genome–wide significance of 5×10^–8. For the first time, five loci were reported to be linked with HT. In addition, six susceptibility loci were identified with heterogeneity between GD and HT. Out of them, four loci including HLA–DPB1, CD40, TSHR and TG, were linked with GD, but not with HT; GD had stronger association with HLA–B than HT but reversed association of SLAMF6 was observed. These findings indicate differences in the pathogenesis of HT and GD.