It is nearly a decade since the discovery of the first mutations in mitochondrial DNA associated with mitochondrial encephalomyopathy, and the pace of discovery of new mitochondrial DNA mutations continues unabated. Nuclear gene defects in these disorders have been more difficult to identify; only one is known, but others have been mapped by linkage analysis. The rules governing transmission and segregation of mitochondrial DNA sequence variants are beginning to be unravelled and progress has been made in understanding genotype-phenotype relationships and elucidating mechanisms of pathogenesis.