Following the discovery in the early 1960s that mitochondria contain their own DNA (mtDNA), there were two major advances, both in the 1980s: the human mtDNA sequence was published in 1981, and in 1988 the first pathogenic mtDNA mutations were identified. The floodgates were opened, and the 1990s became the decade of the mitochondrial genome. There has been a change of emphasis in the first few years of the new millennium, away from the "magic circle" of mtDNA and back to the nuclear genome. Various nuclear genes have been identified that are fundamentally important for mitochondrial homeostasis, and when these genes are disrupted, they cause autosomally inherited mitochondrial disease. Moreover, mitochondrial dysfunction plays an important role in the pathophysiology of several well established nuclear genetic disorders, such as dominant optic atrophy (mutations in OPA1), Friedreich's ataxia (FRDA), hereditary spastic paraplegia (SPG7), and Wilson's disease (ATP7B). The next major challenge is to define the more subtle interactions between nuclear and mitochondrial genes in health and disease.