Accumulating evidence suggests that genetic factors have a role in major depressive disorder (MDD). However, only limited MDDrisk loci have been identified so far. Here we perform a meta-analysis (a total of 90,150 MDD cases and 246,603 controls) throughcombing three genome-wide association studies of MDD, including 23andMe (cases were self-reported with a clinical diagnosis ortreatment of depression), CONVERGE (cases were diagnosed using the Composite International Diagnostic Interview) and PGC(cases were diagnosed using direct structured diagnostic interview (by trained interviewers) or clinician-administered DSM-IVchecklists). Genetic variants from two previously unreported loci (rs10457592 on 6q16.2 and rs2004910 on 12q24.31) showedsignificant associations with MDD (P< 5×10 −8 ) in a total of 336,753 subjects. SNPs (a total of 171) with a P<1×10 −7 in the meta-analysis were further replicated in an independent sample (GS:SFHS, 2,659 MDD cases (diagnosed with DSM-IV) and 17,237controls) and one additional risk locus (rs3785234 on 16p13.3, P=1.57 ×10 −8 ) was identified in the combined samples (a total of92,809 cases and 263,840 controls). Risk variants on the identified risk loci were associated with gene expression in human braintissues and mRNA expression analysis showed that FBXL4 and RSRC1 were significantly upregulated in brains of MDD casescompared with controls, suggesting that genetic variants may confer risk of MDD through regulating the expression of thesetwo genes. Our study identified three novel risk loci (6q16.2, 12q24.31, and 16p13.3) for MDD and suggested that FBXL4 and RSRC1may play a role in MDD. Further functional characterization of the identified risk genes may provide new insights for MDDpathogenesis.