Mitochondria are cellular organelles regulating metabolism and cell death pathways. This study examined changes in mitochondrial membrane potential (deltapsim) throughout the stages of preimplantation development in mouse embryos conceived either in vivo or in vitro and human embryos donated to research from IVF. Embryos stained with the deltapsim-sensitive dye (JC-1) were quantified for the ratio of high- to low-polarized mitochondria using a deconvolution microscope. Overall, mouse zygotes and early embryos contain a subset of high-polarized mitochondria with a progressive increase in the ratio of deltapsim observed with increasing cleavage. A transient increase in the ratio of high to low deltapsim was observed in in vivo fertilized 2-cell stage embryos, coincident with embryonic genome activation in the mouse, but not in 2-cell embryos obtained through IVF. We further observed that arrested mouse 2-cell embryos possessed an increased ratio of deltapsim compared with non-arrested embryos. In human 8-cell embryos we observed an increased ratio of high- to low-polarized mitochondria with increasing degrees of embryo fragmentation. We concluded that the pattern of mitochondrial membrane potential progressively changes throughout preimplantation development, and that an aberrant shift in deltapsim could contribute to, or is associated with, decreased developmental potential.