The rapidly expanding list of human diseases due to lesions of mitochondrial DNA includes myopathies, encephalopathies, cardiomyopathies, or various combinations of the latter, leading to multisystem disorders, which can also affect visceral organs. Five maternally inherited diseases, mainly affecting muscle and brain, are due to point mutations of mitochondrial genes encoding either respiratory chain polypeptides or transfer RNAs. On the other hand, three sporadic entities, Chronic Progressive External Ophthalmoplegia, Kearns-Sayre syndrome, and Pearson's pancreas-bone marrow syndrome, are due to single large-scale deletions of mitochondrial DNA. In addition, multiple deletions are the molecular hallmark of familial encephalomyopathies, inherited as either autosomal dominant or autosomal recessive traits. Finally, tissue-specific depletion of mitochondrial DNA was found in an autosomal recessive disease affecting either muscle, liver, kidney, or a combination of the three. Point mutations and slipped mispairing during, or impairment of, mitochondrial replication are likely mechanisms involved in the pathogenesis of these lesions.