Multicellular organisms comprise a variety of cell types that have the same genotype but distinct phenotypes. This diversity is possible because of the establishment of a specific epigenetic landscape that stabilizes gene expression profiles that are exclusive for a particular cell type. Accumulating data indicate that the maintenance, loss, and reacquisition of pluripotency are dynamically regulated by epigenetic alterations evoked by a subset of cellular factors. A better understanding of the epigenetic mechanisms involved in stem cell biology and differentiation will improve our ability to use these cells in the clinical context. Here we review current insights into the epigenetic mechanisms implicated in embryonic development and the induction of pluripotency.