Embryonic stem cells, derived from the inner cell mass of blastocyst stage embryos prior to implantation, remain pluripotent and self-renewing due to both their inherent properties and the culture conditions in which they are propagated. Recent study of the genetic and epigenetic mechanisms that underlie pluripotency in embryonic stem cells has revealed that mouse and human embryonic stem cells have a number of key features in common; however, our knowledge of this area is incomplete. Detailed analyses of mouse and human embryonic stem cells have revealed a number of differences whose significance is not yet understood. An improved knowledge of the molecular underpinnings of embryonic stem cell properties will be required if these cells are to be utilized as part of cell-based therapies. This chapter offers a review of the current understanding of the molecular mechanisms of pluripotency in human and mouse embryonic stem cells. We also describe insights produced by the use of alternate strategies for production of pluripotent cells, such as somatic cell nuclear transfer and direct reprogramming of terminally differentiated somatic cells.