In few areas of medicine has progress been more spectacular than in the field of mitochondrial diseases, especially those related to mtDNA mutations. Much remains to be done, however, and this brief review discusses the following areas of research where progress has been more limited or data are still controversial: (1) the molecular basis of respiratory-chain defects due to nuclear DNA mutations; (2) defects of mitochondrial protein importation; (3) defects of intergenomic signalling; (4) pathophysiology of mtDNA-related disorders; (5) ageing and age-related neurodegenerative diseases; (6) therapy; and (7) genetic counselling.