Genome-wide epigenetic modification plays a pivotal role in regulating gene expression through chromatin structure and stability, tissue-specific and embryonic developmental specific gene regulation, and genomic imprinting. Mechanisms include chromatin remodeling through histone modification and DNA methylation, RNA associated gene silencing and chromosome inactivation, and genomic imprinting. These epigenetic mechanisms provide an added layer of transcriptional control of gene expression beyond those associated with variation in the sequence of the DNA. Variation in epigenetic regulation helps explain genetic diversity, but significant changes in epigenetic regulation can produce diseases. Advances in understanding epigenetic mechanisms have been accompanied by new therapeutic options and targets for treatment. This review focuses on a basic understanding of epigenetics and some of the diseases associated with epigenetic alterations.