In mammalian species, the mitochondrial genome is between 16.2 and 16.7kb in size and encodes key proteins associated with the cell's major energy-generating apparatus, the electron transfer chain. The maternally inherited mitochondrial genome has, until recently, been thought to be only involved in the production of energy. In this review, we analyse how the mitochondrial genome influences the developing embryo and cellular differentiation, as well as fetal and offspring health and wellbeing. We make specific reference to two assisted reproductive technologies, namely mitochondrial supplementation and somatic cell nuclear transfer, and how modulating the mitochondrial content in the oocyte influences embryo viability and the potential to generate enhanced offspring for livestock production purposes. We also explain why it is important to ensure that the transmission of only one population of mitochondrial (mt) DNA is maintained through to the offspring and why two populations of genetically distinct mitochondrial genomes could be deleterious. Finally, we explain how mtDNA influences chromosomal gene expression patterns in developing embryos and cells primarily by modulating DNA methylation patterns through factors associated with the citric acid cycle. These factors can then modulate the ten-eleven translocation (TET) pathway, which, in turn, determines whether a cell is in a more or less DNA methylated state.