To verify if the peptide preparation <<Cortexin>> can be used to treat pathological processes in CNS during perinatal ontogenesis, registration and analysis of a series of physiological indicators (EMG, ECG, respiration, vagosympathetic balance) were carried out in control infant rats and in a perinatal hypoxic-is- chemic (HI) brain injury rat model. Ischemic brain injury was induced in 7-day-old rats by ligation of the left general carotid artery (under ether anesthesia) followed by keeping the animals in hypoxic gas cham- ber containing 8 % of oxygen and 92 % of nitrogen (day 1 of the experiment). One hour after the exposure to hypoxic conditions the rats of the experimental group were treated with intraperitoneal injections of cortexin at a dose of 1 mg/kg. The drug was injected daily for 10 days. Both control and non-treated ani- mals (with HI brain injury induced) were given the physiological solution. Examinations carried out on days 10 and 30 after operation revealed a lag in the body weight gain in non-treated rats as compared to control animals as well as statistically significant differences in intensity and spectral structure of EMGs between these groups. EMG of the rats.treated with cortexin showed a transient improvement of its spect- ral structure but not of the amplitude on day 10. On day 30 the positive effect of cortexin, as observed earlier, was not revealed. Respiration rate in both treated and non-treated rats was higher than in the control. Heart beat rate in operated rats was not altered, but non-treated animals on day 30 had a tendency towards its depression. The analysis of heart rate variability (HRV) showed that 10 days after trauma both treated and non-treated rats had a statistically significant shift of vagosympathetic balance towards the prevalence of parasympathetic influences. On day 30 cortexin treatment gave a positive effect whereas in non-tre- ated rats a shift of vagosympathetic balance occurred towards the prevalence of humoral, metabolic, and sympathetic influences. Administration of cortexin to intact infant rats leads to appreciable disturban- ces of vagosympathetic balance, heart rhythm, and, to a lesser extent, respiration rhythm and may cause steady disturbances of somatic and autonomic nervous system activity.