Embryogenesis is a complex process that is controlled at various levels. As new discoveries are made about molecular mechanisms that control development in other species, it is apparent that these same mechanisms regulate pig embryogenesis as well. Methylation of DNA and modification of histones regulate transcription, and mechanisms such as ubiquitinization, autophagy and microRNAs regulate development post-transcriptionally. Each of these systems of regulation is highly dynamic in the early embryo. A better understanding of each of these levels of regulation can provide tools to potentially improve the reproductive process in pigs, to improve methods of creating pig embryos and cloned embryos in vitro, and to provide markers for predicting developmental competence of the embryo.