The principles of mitochondrial genetics have evolved over the past 20 years. Careful identification of large pedigrees that were consistent with maternal inheritance has permitted detailed clinical and genetic investigations. Myoclonic epilepsy and ragged-red fiber (MERRF) disease has been a model disease for the application of these principles. MERRF is caused by an A to G mutation of the mitochondrial tRNA(Lys) at position 8344. The mutation is maternally inherited and heteroplasmic. Disease manifestations are dependent on replicative segregation of mutant and wild type mitochondrial DNAs and on the threshold effect. Characterization of the clinical, physiological, biochemical, and genetic manifestations of this disease has provided a better understanding of how to diagnose and manage oxidative phosphorylation diseases which are caused by mutations in the mitochondrial DNA.