TSSK6 is a member of the testis-specific serine/threonine kinase family. Male Tssk6 knockout mice are infertile owing to spermatogenic impairment, including sperm count reduction, a decrease in motile sperm number and motility rates, and an increase in the number of sperms with abnormal morphology. We investigated the possible association between variations of the TSSK6 gene and spermatogenic impairment in humans. Mutation screening of TSSK6 was carried out in 519 patients with azoospermia (n = 273) or severe oligozoospermia (n = 246) and in 359 controls with normozoospermia by denaturing high-performance liquid chromatography and DNA sequencing. The frequencies of alleles and genotypes of gene polymorphism were compared between patients and controls. A novel triallelic polymorphism in TSSK6, c.822+126T>G/C, was identified. The frequencies of genotype TT and allele T were increased dramatically in infertile patients compared with controls, whereas genotype TG, allele G and allele C frequencies were significantly higher in controls than in patients. Further study revealed that the allele C frequency of controls was remarkably higher than that of patients with oligospermia. Our findings, for the first time, suggested an association of c.822+126T>G/C in TSSK6 with spermatogenic impairment in humans in which allele T may be a risk factor for male infertility, while alleles C and G may decrease susceptibility to male infertility.