The ability of pluripotent stem cells to differentiate into all cell types of an organism has received widespread attention in basic and clinical research and holds tremendous potential for pharmacologic and medical applications. In this review, we provide an overview of the factors and pathways involved in pluripotency and discuss a possible mechanism underlying genetic reprogramming using defined transcription factors. We specifically address the association between core transcription factors (e.g. Oct4, Sox2 and Nanog) and the cellular machinery (e.g. chromatin remodeling complex, DNA methylation, microRNA and X chromosome inactivation), which has an important role in cell fate determination.