Embryonic stem cells (ESCs) are pluripotent cells with an indefinite replication potential and an ability to differentiate into a variety of cell lineages, holding a great promise for regenerative medicine and biological research. The genome and transcriptome of ESCs have been extensively examined in order to decipher their self-renewal and differentiation mechanisms. Global transcriptional profiling allows the identification of genes expressed differentially or uniquely in ESCs and the elucidation of the molecular signatures. Comparative genomics and transcriptomics help to explore evolutionarily conserved and divergent transcriptional patterns and functional landscape of ESCs, and identify fundamental and species-specific mechanisms controlling the pluripotency. Chromosomal mapping of the transcriptome demonstrates the coexpression of neighboring genes along the chromosome and highlights their dynamic changes in response to ESC differentiation. Epigenetic analysis reveals methylation patterns and microRNA profiles unique to ESCs. In this article, various aspects of genomic and transcriptomic studies on ESCs are reviewed, and important findings regarding ESC self-renewal and differentiation are highlighted and discussed.