Human oocytes have an abundance of mitochondria that have their own genome. Mitochondrial functions are exerted through evolutionarily-developed interactions between the nucleus and mitochondria. Since 1996, fertility clinics have practiced various types of germline mitochondrial DNA (mtDNA) modification that alter the composition of mtDNA copies in oocytes or zygotes using micromanipulation. Experimental reproductive medicine has primarily intended to treat intractable infertility and has been used to prevent the maternal transmission of a pathogenic mtDNA mutation to offspring. In some cases, it has helped parents have a healthy genetically-related child; in others, it has resulted in miscarriages, aneuploid fetuses, or developmental disorders in the offspring. Adverse events have raised ethical controversy, leading to restrictive or prohibitive policies in the USA and China. Conversely, the UK recently became the first nation to explicitly permit two types of germline mtDNA modification (termed mitochondrial donation) for the sole purpose of preventing serious mitochondrial disease in offspring. The aim of this review is three-fold: first, to reshape the medical concept and evolution of germline mtDNA modification, while revisiting 14 clinical cases. Second, to analyse the legality of mtDNA modification, focussing on 16 Western countries. Finally, to consider the ethical aspects, including permissible cases, reproductive options, use of preimplantation and prenatal testing, and the humane follow-up of resultant children. The clinical use of germline mtDNA modification will likely become legal, at least for use in preventative medicine, in some countries. However, the potential clinical, ethical, and evolutionary implications mean that caution is required when considering its wider application.