The mitochondrial myopathies or encephalomyopathies with known biochemical defects can be divided into 5 groups: (1) defects of mitochondrial transport, such as CPT deficiency or carnitine deficiencies; (2) defects of substrate utilization, such as PDHC deficiency or defects of beta-oxidation; (3) defects of the Krebs cycle, such as fumarase deficiency; (4) defects of oxidation-phosphorylation coupling, such as Luft disease, and (5) defects of the respiratory chain. These disorders are reviewed, with particular emphasis on the defects of the respiratory chain. Defects of complex I, III and IV show remarkable clinical and biochemical heterogeneity. All 3 complexes contain some subunits encoded by mtDNA and others encoded by nuclear DNA. At least some of the cytoplasmically made subunits appear to be tissue specific and may be developmentally regulated, thus explaining the genetic heterogeneity of these disorders.