Treatment strategies in mitochondrial diseases consist of several drugs that diminish the deleterious effects of the abnormal respiratory chain function, reduce the presence of toxic agents or correct deficiencies in essential cofactors. In this study we evaluated the monitoring of tocopherol, carnitine and ubiquinone concentrations in a group of paediatric patients during a follow-up period of 18 months and the response to treatment of these patients by means of the determination of blood lactate, plasma alanine and oxygen consumption by lymphocytes in relation to the clinical status of the patients. Tocopherol, carnitine and ubiquinone concentrations were easily corrected with therapy. Blood lactate proved the best biochemical tool to assess the response to treatment in paediatric patients. According to our results, improvement or stabilization of the clinical course seems to be more related to the biochemical or molecular defect than to the effectiveness of the treatment.