Phosphorus magnetic resonance spectra of resting muscle were obtained from 4 patients with alternating hemiplegia of childhood. All patients had abnormally high resonance intensities from inorganic phosphate and an abnormally low calculated cytosolic phosphorylation potential. Two of the 4 patients had abnormally low resonance intensities from phosphocreatine and an abnormally high calculated cytosolic free adenosine diphosphate concentration. These abnormalities are indicative of mitochondrial dysfunction. The combination of a central nervous system disorder and evidence of mitochondrial dysfunction in muscle suggests that alternating hemiplegia of childhood may represent a previously unrecognized phenotype of mitochondrial disease.