The aim of the investigation is to assess the quantity of brain-derived neurotrophic factor (BDNF), glial cell line-derived neurotrophic factor (GDNF) and neuron specific enolase (NSE) in plasma of newborns with perinatal hypoxic damage of CNS. Materials and Methods. Neurotrophic factors and NSE enzyme concentrations in plasma of newborns (gestation age 31–42 weeks) was studied. The main groups consisted of newborns with the symptoms of perinatal CNS damage (group 1 — with convulsive states, group 2 — with the signs of severe perinatal CNS damage), diagnosed according to physical examination, evaluation of the neurological status dynamics and neurosonographic studies. Control group included healthy neonates. Concentration of BDNF, GDNF (R&D Systems, USA) and NSE enzyme (Vector Best, Russia) was determined by ELISA kit during hospitalization and on day 10–14 after the rehabilitation therapy. Results. Carried out experiments revealed the significant increase of NSE concentration in plasma of newborns with convulsive states. The higher levels of this enzyme were detected in infants with severe perinatal CNS damage. Moreover, BDNF concentration significantly increases in plasma of patients with the symptoms of severe CNS damage in the period following rehabilitation therapy. These experiments also demonstrate the inverse correlation between BDNF and GDNF levels. It was shown the important prognostic value of BDNF and NSE determination in plasma of newborns with CNS injury. Conclusion. The most diagnostic value for assessing the severity of brain damage in early neonatal period is associated with measurements of NSE and BDNF concentrations in plasma, which allows to use these markers immediately after birth and before the development of neurological symptoms.