Epigenetic modifications change gene expression in such a way that gene action is affected without change in DNA sequence. Several genes playing crucial roles in spermatogenesis are known to be epigenetically regulated. Epigenetic modifications affect spermatogenesis, and aberrant epigenetic modifications at certain loci are linked to male infertility. Epigenetic modifications could be the mechanism by which several environmental hazards such as exposure to endocrine disruptors affect spermatogenesis. Imprinting as an effect of changes in the epigenome has the potential to change gene expression up to several generations leading to inheritance of the modified phenotype. In the present review, we have gathered evidence that epigenetic modifications affect spermatogenesis and contribute to male infertility.