Tissue development and maintenance rely on coordinated interactions of individual cells. The correct composition of the three-dimensional cell neighbourhood is essential. However, often the details of the spatial arrangement of the cells are unknown and the processes underlying its establishment and maintenance are understudied. We focus on the development of the mouse blastocyst. Just before implantation, the cells of the inner cell mass differentiate into embryonic or extraembryonic precursor cells. Hallmarks of the cell fate decision are the expression levels of the two transcription factors NANOG and GATA6 in the cells. We quantitatively analysed the three-dimensional spatio-temporal arrangement of cells with different expression levels in ICM organoids and mouse embryos. We describe a so far unknown local clustering of cells with comparable expression levels that is already present at the early blastocyst stage. The cell fate decision occurs through a transition from such a local to a global pattern. Using mathematical modelling, we identify different mechanisms that could generate the observed patterns. Our results highlight the importance of analysing the three-dimensional cell neighbourhood while investigating cell fate decisions during early mouse embryonic development.