Infertility is a major reproductive health problem affecting 10% to 15% of couples, with approximately equal contributions. Spermatogenesis is a dynamic and multistep process of male germ cell proliferation and differentiation by which spermatozoa are produced from primordial germ cells. The causes of spermatogenic defects in infertile men are multifactorial and many environmental, nutritional, behavioral and genetic factors affect male infertility. In most of the infertile cases, the underlying mechanisms remain obscure. Genomics and proteomics offer new tools for better understanding the genetics of male infertility. The current review provides insights into the plausible chromosomal, genetic and epigenetic alterations, which may result into infertile phenotype.