Fkbp6 has been proved to be a new component of synaptonemal complexes and be involved in homologous chromosomes pairing and male infertility in mice. To explore the possible association between variations in the FKBP6 gene and impaired spermatogenesis in human, mutation screening of all the eight exons and the intron/exon boundaries of the gene was performed in 323 patients with azoospermia or severe oligozoospermia and 205 fertile controls by denatured HPLC and DNA sequencing. As a result, four novel and one known single nucleotide transitions were identified, including c.58-2A>G, c.111C>T, c.156G>T, c.594G>A, and c.216C>A (rs3750075). The frequencies of genotype CA, allele A of c.216C>A and haplotype 'GAG' consisting of c.156G>T, c.216C>A, and c.594G>A were significantly lower in infertile patients than those in controls. These findings suggest that the FKBP6 gene may play a role in modifying the susceptibility to idiopathic spermatogenic impairment in human and propose that the allele A of c.216C>A seems to be a protective factor for the development of male infertility.