A complex prospective clinical and biochemical study was carried out in 252 children with perinatal encephalopathy during the 1st year of their life. The lipid peroxidation process, antioxidant system, lysosomal enzymes, phospholipid compound of thrombocyte membranes were studied. The lipid peroxidation process and lysosomal enzymes activation as well as a decrease of antioxidant defense level have been found. Membrane destabilization processes in the children with perinatal encephalopathy correlated with a character of hypoxic influence (acute, chronic, combined), a degree of severity and clinical manifestations of the pathology, and disease stage. Clinical and biochemical efficacy of antioxidant mexidol (0.1-0.2 ml/kg of the body weight intravenously for 10 days) and inhibitor of lysosomal enzymes contrical (1000 U/kg intravenously for 3-5 days) in the infants with perinatal CNS damages is claimed.