Embryonic stem (ES) cells, like all cell types, are defined by their unique transcriptional signatures. The ability of ES cells to self-renew or exit the pluripotent state and enter differentiation requires extensive changes in gene expression. Gene regulatory programs governing each cell fate must remain sufficiently malleable so that expression of only a handful of transcriptional activators can override the pre-existing state to specify, restrict and stabilize the new state. Here, we discuss recent advances in our understanding of how gene regulatory proteins control stem cell-specific transcriptional outputs.