FAS, together with FASLG, triggers germ cell apoptosis, which occurs in various stages of mammalian testicular development. Single nucleotide polymorphisms (SNP) in the promoter regions of these two genes can influence their transcriptional activities and result in abnormal cell apoptosis, thus leading to spermatogenesis impairment. Therefore, it is reasonable to postulate that FAS and FASLG SNP may be associated with idiopathic azoospermia or severe oligozoospermia. To test this hypothesis, the distributions of FAS -1377G/A and -670A/G SNP and FASLG -844C/T SNP were studied in Han Chinese men. These SNP were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in 203 infertile men with idiopathic azoospermia or severe oligozoospermia and in 246 proven fertile controls. Frequencies of FASLG -844CC, CT and TT genotypes among infertile men were significantly different from those among controls (P = 0.024). Men with FASLG -844TT genotype had an increased risk of idiopathic azoospermia or severe oligozoospermia compared with those with CC and CT genotype (odds ratio 2.72, 95% confidence interval 1.25-5.93). The results suggest that FASLG -844C/T SNP may be a genetic predisposing factor of idiopathic azoospermia or severe oligozoospermia among Han Chinese men.