Transcriptional regulators and epigenetic modifiers play crucial roles throughout development to ensure that proper gene expression patterns are established and maintained in any given cell type. Recent genome-wide studies have begun to unravel how genetic and epigenetic factors maintain the undifferentiated state of embryonic stem cells while allowing these cells to remain poised to differentiate into somatic cells in response to developmental cues. These studies provide a conceptual framework for understanding pluripotency and lineage-specification at the molecular level.