Epigenetics, the alteration of gene expression without any changes in DNA sequence, has been established to be heritable. Depending upon where epigenetic marks are located, epigenetic mechanisms can influence gene expression patterns which play vital roles in development and disease. Currently, epigenetic programming in mammals includes DNA methylation and histone modifications, including their variants and RNA-associated silencing. First, DNA methylation plays an important role in genomic imprinting and X-chromosome inactivation during embryonic development and in several diseases such as cancer, ATRX syndrome, Rett syndrome, and male infertility in humans. Second, modifications of both core and variant histones have been shown to influence gene regulation through changes in nuclear chromatin structure. Lastly, non-coding RNAs knock down gene expression through diverse mechanisms including the siRNA pathway. In this review, we summarize the aforementioned epigenetic phenomena first in general and then as it relates specifically to reproduction associated with male germ cells.