Mortality rates in males are higher than in females at every age, including as newborns. Although sexual dimorphisms are usually attributed to hormonal influences, differences observed at early embryonic stages can’t be accounted for in this way. For example, male embryos have a higher growth rate at preimplantation stages, before overt sexual differentiation and exposure to sex hormones. X inactivation, a drastic epigenetic event exclusive to females, likely affects the embryonic transcriptome and epigenome in a sex-specific manner. Thus, male and female genomes are epigenetically poised for their divergent pathways early on. To determine whether there is differential expression at preimplantation stages, we derived male and female mouse embryonic stem (ES) cell lines and performed RNA-sequencing. When XY and XX cell lines were compared, over 400 coding genes were differentially expressed (ɑ< 0.01). A substantial number of these are transcription factors and epigenetic enzymes that are predicted to be dosage sensitive, indicating that there are regulatory differences between male and female embryos that depend solely on their chromosomal composition. In addition, we found more than 300 non-coding RNAs that were sex-biased (ɑ< 0.01). RNA-seq results were validated by qPCR and effects of differentially expressed transcription factors were confirmed with luciferase assays. To determine whether these expression differences translated into epigenomic differences, we conducted focused chromatin immunoprecipitation analyses and observed significant sex-dependent variation in chromatin accessibility in specific genes. We are exploring whether these sexual dimorphisms predict distinctions in response to environmental signals and whether they foreshadow sex-specific health-related outcomes after birth. Our results will have implications in understanding the developmental origins of disease, will impact disease treatment and stratification and, importantly, may have significance in the field of regenerative medicine. Furthermore, understanding sex biases in transcription and epigenetic status will provide insights into sex differences in susceptibilities to and protection from diseases.