In recent years new descriptions of basic structural and functional aspects of mitochondrial DNA have furthered our understanding of the role mitochondrial genome mutations play in human diseases. These mutations can be classified in two large groups: deletions and duplications, and point mutations. Deletions are typically sporadic and patients that carry them have varying types of symptoms. Point mutations, which affect genes that code tRNAs or genes that code mitochondrial respiratory chain proteins, are inherited through the maternal line and are also associated to a wide range of clinical signs. Some alterations are inherited according to a Mendelian pattern, involving multiple deletions and duplications of mitochondrial DNA caused by a defect in a factor coded by the nuclear genome and implicated in the regularization and replication or transcription of the mitochondrial genome. These changes are also related, directly or indirectly, to aging and to such common diseases as maternally transmitted diabetes.