The mouse inner cell mass (ICM) segregates into the epiblast and primitive endoderm (PrE) lineages coincident with implantation of the embryo. The epiblast subsequently undergoes considerable expansion of cell numbers prior to gastrulation. To investigate underlying regulatory principles, we performed systematic single-cell RNA sequencing (seq) of conceptuses from E3.5 to E6.5. The epiblast shows reactivation and subsequent inactivation of the X chromosome, with Zfp57 expression associated with reactivation and inactivation together with other candidate regulators. At E6.5, the transition from epiblast to primitive streak is linked with decreased expression of polycomb subunits, suggesting a key regulatory role. Notably, our analyses suggest elevated transcriptional noise at E3.5 and within the non-committed epiblast at E6.5, coinciding with exit from pluripotency. By contrast, E6.5 primitive streak cells became highly synchronized and exhibit a shortened G1 cell-cycle phase, consistent with accelerated proliferation. Our study systematically charts transcriptional noise and uncovers molecular processes associated with early lineage decisions. Display omitted •A high-resolution scRNA-seq map of mouse from peri-implantation to early gastrulation•Symmetry breaking genes and bivalent chromatin are linked to lineage fate at E4.5•X chromosome inactivation correlates with Rlim and anticorrelates with Dnmt3a and Zfp57•Polycomb targets are repressed in the E6.5 epiblast and activated in the primitive streak Mohammed et al. chart mouse embryonic development from implantation to early gastrulation at single-cell resolution. They describe regulatory processes associated with lineage commitment. An increased level of transcriptional noise is observed prior to lineage commitment, an observation that provides fresh insights into cell fate decision-making processes.