Inner cell mass (ICM) cells of a blastocyst, the source of embryonic stem (ES) cells, are characterized by their unique ability to give rise to all cell types in adult organisms. The epigenomes of germ cells and developing zygotes undergo extensive reprogramming to acquire such a pluripotent state. A major reprogramming event during early embryonic development is the erasure and subsequent re-establishment of patterns of methylation at the 5-position of cytosine (5mC). The recent demonstration that Ten-eleven translocation family proteins, Tet1-3 have the capacity to convert 5mC to 5-hydroxymethylcytosine (5hmC) raises the possibility that 5hmC may act as an distinct epigenetic state contributing to dynamic changes in DNA methylation and transcriptional regulation during embryonic development. In ES cells, Tet1 is highly expressed and 5hmC is present at relatively high levels compared to most differentiated cells, but the functional significance of Tet1 and 5hmC in these pluripotent cells are not clear. Recently, a flurry of papers that profile the distribution of Tet1 and/or 5hmC across the genome of mouse ES cells provide new insights into the role of Tet proteins and 5hmC in regulating expression of genes related to pluripotency and cellular differentiation. Through integrative analyses of datasets from different groups, we reveal the common Tet1 and 5hmC targets in undifferentiated mouse ES cells, which suggest that Tet1 may play a key role in orchestrating the balance between pluripotent and lineage committed states.