Coenzyme Q10 content, pathology evaluation, and electron transport chain (ETC) enzyme analysis were determined in muscle biopsy specimens of 82 children with suspected mitochondrial myopathy. Data were stratified into three groups: "probable" ETC defects, "possible" ETC defects, and disease controls. Muscle total, oxidized, and reduced coenzyme Q10 concentrations were significantly decreased in the probable defect group. Stepwise logistic regression indicated that only total coenzyme Q10 was significantly associated with probable ETC defect. Receiver operator characteristic (ROC) analysis suggested that total muscle coenzyme Q10 was the best predictor of an ETC complex abnormality. Determination of muscle coenzyme Q10 deficiency in children with suspected mitochondrial disease may facilitate diagnosis and encourage earlier supplementation of this agent.