Male factor infertility affects one-sixth of couples worldwide, and non-obstructive azoospermia (NOA) is one of the most severe forms. Our previous genome-wide association study (GWAS) identified three susceptibility loci for NOA in Han Chinese men. Here we test promising associations in an extended three-stage validation using 3,608 NOA cases and 5,909 controls to identify additional risk loci. We find strong evidence of three NOA susceptibility loci (Po5.0 Â 10 À 8 ) at 6p21.32 (rs7194, P ¼ 3.76 Â 10 À 19 ), 10q25.3 (rs7099208, P ¼ 6.41 Â 10 À 14 ) and 6p12.2 (rs13206743, P ¼ 3.69 Â 10 À 8 ), as well as one locus approaching genome-wide significance at 1q42.13 (rs3000811, P ¼ 7.26 Â 10 À 8 ). In addition, we investigate the phenotypic effect of the related gene (gek, orthologous to CDC42BPA) at 1q42.13 on male fertility using a Drosophila model. These results advance our understanding of the genetic susceptibility to NOA and provide insights into its pathogenic mechanism.