The preimplantation mouse embryo consists of three lineages: trophectoderm, primitive endoderm (PrE) and epiblast (Epi), which will become the future foetus. PrE and Epi precursors are initially present in a ‘salt and pepper’ distribution within the blastocyst and subsequently sort into two distinct layers but what controls this segregation? Here, Berenika Plusa and colleagues show that atypical protein kinase C (aPKC) couples cell sorting with cell fate progression in the mouse blastocyst (p. 4311). They first show that aPKC is enriched in PrE precursors prior to cell sorting. This enrichment, they report, is dependent on FGF signalling and the acquisition of PrE fate. Importantly, RNAi knockdown or chemical inhibition of aPKC impairs PrE-Epi segregation. Finally, the authors demonstrate that inhibition of aPKC also compromises the maturation of PrE cells; embryos treated with aPKC inhibitor fail to form a PrE layer and concomitantly fail to develop a polarised apical surface. The authors thus propose that aPKC links cell sorting with the progression of cell differentiation in the blastocyst.