After fertilization, the mammalian conceptus undergoes cleavage, a process of cell proliferation in the absence of interphase growth. It is not known when cleavage ends and gives way to fully replicative cell cycles with a stable nucleo-cytoplasmic ratio. We have used two-photon excitation and confocal microscopy to measure directly volumes and nucleo-cytoplasmic ratios of whole murine concepti and their individual constituent blastomeres during pre-implantation development up to the early uterine attachment stage (day 5). We show that the total cytoplasmic volume of the conceptus remains constant during pre-implantation development, and that the average nucleo-cytoplasmic ratio increases exponentially throughout the same period. Data from individual blastomeres show that both volume and nucleo-cytoplasmic ratio diverge in the inner and outer subpopulations evident from the 16-cell stage (fifth developmental cycle) onwards. Cells from emergent outer trophoblast populations are larger and have smaller nucleo-cytoplasmic ratios than those from emergent inner pluriblast populations. Moreover, the nucleo-cytoplasmic ratio of the trophoblast appears to be stabilizing, suggesting that for this subpopulation cleavage may end at the 16–32-cell transition. Putative hypoblast and epiblast cell subpopulations within the pluriblast were not distinguishable by volume or nucleo-cytoplasmic ratio. Embryonic stem cell volume was higher than that of either cell subpopulation of expanded blastocysts, and their nucleo-cytoplasmic ratio was similar to that of trophoblast cells.