Mitochondrial DNA (mtDNA) mutation is associated with serious human disorders and affects multiple organs and tissues with high-energy requirements. Since the transmission of mtDNA is complex and is not fully understood, an accurate estimation of mtDNA disease transmission by preimplantation genetic diagnosis (PGD) or by prenatal diagnosis (PND) remains challenging. Recently, nuclear transfer techniques, including maternal spindle transfer (MST), pronuclear transfer (PNT) and polar body transfer (PBT), have shown the promising results. These methods avoid the transmission of mutated mtDNA from mother to offspring, and are collectively known as the mitochondrial replacement therapy (MRT). Further, the United Kingdom Parliament approved the Human Fertilisation and Embryology Authority (HFEA) to grant licenses for experimental use of MST and PNT in humans in 2015. Thus, a new era of assisted reproductive technology (ART), in which cures can be provided at the gamete or early zygote stages, is realistically approaching. In this review, we summarize the methods and the challenges confronting the clinical application of MRT.