Differentiation of human embryonic stem cells (hESCs) provides a unique opportunity to study the regulatory mechanisms that facilitate cellular transitions in a human context. To that end, we performed comprehensive transcriptional and epigenetic profiling of populations derived through directed differentiation of hESCs representing each of the three embryonic germ layers. Integration of whole-genome bisulfite sequencing, chromatin immunoprecipitation sequencing, and RNA sequencing reveals unique events associated with specification toward each lineage. Lineage-specific dynamic alterations in DNA methylation and H3K4me1 are evident at putative distal regulatory elements that are frequently bound by pluripotency factors in the undifferentiated hESCs. In addition, we identified germ-layer-specific H3K27me3 enrichment at sites exhibiting high DNA methylation in the undifferentiated state. A better understanding of these initial specification events will facilitate identification of deficiencies in current approaches, leading to more faithful differentiation strategies as well as providing insights into the rewiring of human regulatory programs during cellular transitions. Display omitted •Epigenetic and transcriptional dynamics in hESCs and hESC-derived populations•Lineage-specific remodeling at regions bound by OCT4, SOX2, and NANOG in hESCs•Germ-layer-specific switch to H3K4me1 or H3K27me3 at sites of high DNA methylation•Epigenetic dynamics frequently precede transcriptional activation The epigenetic and transcriptional landscapes of three cell types representing each embryonic lineage derived from human embryonic stem cells are profiled, revealing distinct histone modification and DNA methylation dynamics that accompany lineage specification.