We studied three patients with Leigh's syndrome (LS) and cytochrome c oxidase (COX) deficiency. Biochemical studies in brain, muscle, heart, liver, kidney, and fibroblasts disclosed a generalized COX deficiency. Kinetic studies of COX activity in brain mitochondria showed a low Vmax and a normal Km for reduced cytochrome c. Immunologic studies showed decrease of all COX subunits studied, without a specific defect of any one of them. Southern blot analysis excluded large deletions of mitochondrial DNA (mtDNA) but revealed a generalized increase in mtDNA quantity. Although Northern blot analysis showed no alteration in the 12 COX subunit mRNAs studied, two of three patients showed a decreased steady state rate of COX transcription in brain. COX deficiency in LS thus appears to be related to a decreased amount of otherwise normal COX holoenzyme.