Two different isoforms of subunit VIIa have been found in cytochrome c oxidase isolated from human skeletal muscle. The first 22 residues of the N-terminal amino acid sequences showed 5 differences. Our results provide the first conclusive evidence for the existence of cytochrome c oxidase isoenzymes in man. Since the two cytochrome c oxidase isoforms were both present in skeletal muscle tissue, though not necessarily in the same cell type, this suggests that human cytochrome c oxidase isoforms are not strictly tissue-specific. These findings may have important implications for the elucidation of genetic diseases in man in which a deficiency of cytochrome c oxidase is restricted to certain tissues.