BACKGROUND Genetic mechanisms are associated with male infertility, but the association with non-obstructive azoospermia (NOA) remains unclear. Mutations in the chloride channel accessory 4 (CLCA4) gene have been shown to have a role in male infertility. The aim of this study was to investigate the associations between single nucleotide polymorphisms (SNPs) of the CLCA4 gene and NOA in a Chinese Han population of Northeast China using combined targeted gene capture next-generation sequencing and bioinformatics analysis. MATERIAL AND METHODS The study group included 100 men with NOA, and there were 100 normal controls. Targeted gene capture next-generation sequencing was performed combined with bioinformatics analysis. Ten CLCA4 SNPs were screened in the cases of NOA and control subjects. The associations between SNPs and NOA were analyzed. RESULTS Six SNPs, c.390C>T (rs190628533), c.1474A>G (rs2231599), c.2105C>G (rs757773924), c.2371A>T) (rs759981524), c.956G>A (rs763334876), and c.895T>C (rs79822589) were identified in the study group of cases in NOA but not in control subjects. All CLCA4 SNPs were in Hardy-Weinberg equilibrium. The allele and genotype frequencies of the six SNPs were not significantly different between the study group and the controls. Haplotype analysis showed the existence of two haplotypes, CTAGACTACG and CTCGACTACG, which showed statistical significance of 0.074, and 0.088 between cases of NOA and the controls, respectively. CONCLUSIONS There were no significant associations between CLCA4 SNPs and NOA in men in a Chinese Han population of Northeast China.