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In human, six Arylsulfatase D (ARSD) genes (ARSD A-F) exist, out of which four are clustered on short arm of X-chromosome that are linked with male fertility factors involved in regulating spermatogenesis. Our aim was to find out the role of ARSD gene based on next generation sequencing (NGS), whose role in male infertility still remains obscure. Clinically the case of male infertility was diagnosed on the basis of semen analysis and hormone profile, confirming non-obstructive azoospermia. Karyotype was prepared and microdeletions of Y-chromosome were detected using STS markers. No mutations were identified either in karyotype or using STS markers. Interestingly, the finding of the NGS based analysis revealed four different single nucleotide gene polymorphism (SNP) of ARSD gene rs111939179 C→T, rs73632978 G→A, rs73632977 A→T, rs73632976 C→T in heterozygous conditions. The results enhance our current understanding of the genetic basis of male infertility and provide helpful clues for designing future studies.