To investigate the possible association between variations in the PRDM9 (MEISETZ) gene and impaired spermatogenesis in humans, we screened for mutations in the human PRDM9 gene using DNA from 217 sterile male patients and 162 proven fertile male volunteers. Two single-nucleotide polymorphisms (SNPs), 17353G>T (Gly433Val) and 18109C>G (Thr685Arg), were identified, as well as an intronic SNP, 15549G>T. These SNPs were identified in the heterozygous state in separate patients who demonstrated azoospermia. Neither variant was identified in fertile subjects. Our results suggest that mutations in PRDM9 may cause idiopathic infertility in human males.