The role of mitochondria in remodeling of the donor cell nucleus in cloned animals has gained increased attention, as mitochondria interact in direct or indirect ways with the donor cell nuclear DNA. Mitochondria comprise 1% of the genetic material that is contributed to the developing embryo by the recipient oocyte and provide the energy that is required for embryo development. In this review we compare mitochondria distribution in various species and the importance of mitochondria distribution for embryo development. We also compare the inheritance pattern of mitochondria in cloned embryos that remains unresolved, as the donor cell nucleus is typically transferred with surrounding cytoplasm including mitochondria which become destroyed in some but not all species. We review the role of mitochondria in cloned farm animals with emphasis on nucleo-cytoplasmic interactions and consequences for embryo development.