The coding sequence for the human mitochondrial genome (mtDNA) was published in 1981. Within a decade, the first pathogenic mtDNA mutations were described in humans with sporadic and maternally inherited disease. The last ten years has seen a profusion of reports describing new pathogenic mutations associated with a diverse range of clinical phenotypes. Although we have seen great advances in our understanding of the molecular mechanisms involved in the pathogenesis of mtDNA disease, we are only just beginning to tackle some of the more difficult questions. In this review we describe recent advances in our understanding of mtDNA disease and highlight ways that this knowledge might lead to novel therapies in the future.