We carried out single nucleotide polymorphism (SNP) and mutation analyses of haploid germ cell-specific genes. An analysis of 13 genes associated with male infertility in approximately 300 infertile male patients and approximately 300 male volunteers with proven fertility revealed two mutations that might produce male infertility, and three SNP/mutations associated with male infertility in 13 germ cell-specific genes. These findings strongly support the hypothesis that dysfunction of germ cell-specific genes causes idiopathic human male infertility.