Understanding the molecular mechanisms involved in the control of cell differentiation during embryonic development is currently one of the main objectives of developmental biology. This knowledge will provide a basis for the development of new strategies in the field of regenerative medicine, one of the most promising weapons to fight many human diseases. Cell differentiation during embryonic development is controlled primarily by epigenetic factors, that is, mechanisms involved in the regulation of chromatin structure and gene expression. Here we describe the best known epigenetic modifications, and pathways, mainly focused on DNA methylation and histone modifications, and try to depict the state of art in our knowledge about epigenetic regulation of embryonic stem cell maintenance and differentiation.