There are three cell lineages in the blastocyst stage of human embryo development: trophectoderm, primitive endoderm, and epiblast. Due limited access to human embryos, we have limited understanding of how each lineage come about. We examine the gene expression of 241 single cells from early to late human blastocyst to tease out the gene expression changes. We identify role for MCRS1, TET1, and THAP11 in epiblast formation and their ability to induce naïve pluripotency in vitro. Our method demonstrates that single cell gene expression analysis will further the understanding of human stem cell biology.