Mitochondrial DNA is strictly regulated during oogenesis so that mature oocytes possess sufficient copies to support and promote fertilisation and subsequent developmental events. Poor quality oocytes often have significantly lower numbers of mitochondrial DNA copy, a situation known as mitochondrial DNA deficiency, which frequently affects women of older reproductive age. Mitochondrial DNA deficiency can be overcome by supplementing mitochondrial DNA deficient oocytes with autologous populations of mitochondria at the time of fertilisation. We now describe this approach as mitochondrial intracytoplasmic sperm injection (mICSI), which ensures that the offspring’s genetic identity is not perturbed. Using a pig model of oocyte mitochondrial DNA deficiency, we have shown that the use of mICSI results in improved development to the blastocyst stage, the final stage of preimplantation development. These blastocysts exhibit gene expression profiles that are more similar to those of blastocysts derived from oocytes possessing normal levels of mitochondrial DNA copy number. Importantly, mICSI restricts the expression of genes that are associated with metabolic disorders and are indicative of blastocysts derived from mitochondrial DNA deficient oocytes.