The mammalian blastocyst comprises three lineages – the trophectoderm (TE), the primitive endoderm (PrE) and the pluripotent epiblast (EPI). Decades of work have revealed the transcriptional networks controlling the segregation of these lineages in mice, but more recently human embryos have been directly studied, including by single-cell sequencing. However, comparison of single-cell datasets is complicated by technical differences and biological variability, and the PrE/EPI lineage segregation in the inner cell mass (ICM) has been particularly hard to clarify. Now, Paul Bertone and colleagues present a comprehensive analysis of three previously generated single-cell transcriptome datasets in staged human embryos. The authors first show that an overrepresentation of TE cells obscures existing PrE/EPI distinctions, and then define four high-confidence marker genes per lineage that can be reliably used to classify cells throughout early embryogenesis. Their unified transcription map provides robust transcriptional features of each lineage, and reveals for example that the ICM of the late blastocyst comprises a patchwork of committed and transitory states. Finally, the authors apply their framework to human pluripotent stem cell lines, identifying conditions that support naïve pluripotency in culture. As well as providing a resource for the future and resolving prior discrepancies, the study provides novel insights into the choices made at the beginning of human life.