Background: Male factor infertility that is the cause of about half of the infertility cases, may occur due to azoospermia. Because spermatogenesis defects may lead to non-obstructive azoospermia (NOA), investigating the factors involved in spermatogenesis, including hormones and genes, is one of the most important aspects in understanding the mechanism of NOA in men. Objectives: Male infertility is a complex disorder that affects a large proportion of men, yet many of its causes are unknown. Clarifying its genetic basis may help to identify the causes of infertility and provide effective treatment for patients. Methods: In this case-control study, single nucleotide polymorphisms (SNPs) located in the USP9Y gene were investigated. Accordingly, 100 healthy men and 100 NOA patients were regarded as control and case groups, respectively. Testis tissue samples were taken during the testicular sperm extraction (TESE) procedure, DNA extraction was done, and ARMS PCR was designed and performed. The rs3212292, rs2032597, rs2032604, rs2032598, and rs717268 polymorphisms in the USP9Y gene were analyzed by Tetra-ARMS PCR. Furthermore, the serum levels of sex hormones were assessed by the ELISA technique. Finally, the obtained data were analyzed by SPSS software. Results: According to the obtained results, there was no significant difference in case of genotype frequency of investigated SNPs between the case and control groups (P ≥ 0.05). The mean FSH and LH levels in the control group were relatively lower than the case group (P ≤ 0.05), whereas no significant difference in the mean testosterone level was observed between the two groups (P ≥ 0.05). Conclusions: Polymorphisms of the assessed SNPs showed no effect on the frequency of azoospermia; thus, polymorphisms did not increase the risk of NOA and also did not have a protective effect against the disease. Also, the results showed that the serum levels of FSH and LH increased in NOA patients.