Reports have suggested that a subset of autistic children have mitochondrial or fatty-acid oxidation defects. The metabolic studies from 133 consecutive patients evaluated in a medically-based autism clinic were reviewed to determine the prevalence of elevations in biomarkers for mitochondrial and fatty-acid oxidation defects. Markers for mitochondrialdisorders included standard biomarkers (lactate, alanine) and recently described biomarkers (alanine-to-lysine ratio, creatine kinase, aspartate transaminase). Testing was collected in the morning during a fasting state. If markers were abnormal, repeat testing was recommended. Secondary disorder of fatty acid metabolism such as biotin deficiency, carnitine abnormalities and general increase in fatty acids were ruled out in patients with consistent acyl-caritine elevations. Consistent elevations in biomarkers of energy metabolism were found in independent subsets of children who were evaluated for autism with a high percentage of these children having a history of regression and/or epilepsy. These data lend support to the notion that disorders of energy production may affect a subset of children with autism.