The main aim was to study the characteristics of heart rate variability in 8- and 10-year boys and girls that permanently reside in areas with an increased level of radioactive contamination. The body functions are formed by close interaction of the body and the environment. The adaptive responses of the developing organism are improved at each ontogenetic stage as its contact with the environment become more complex. We found that features of heart rate regulation depend on the area of residence. The contribution of the autonomous circuit of heart rate regulation is increased for 8- and 10-year-old girls from radio-ecologically safe areas (RESA). Based on the principle of functional antagonism this leads to a weakening of the central circuit of regulation. The shift gradient of indicators is higher for 8-year-old girls from radio-ecologically unfavorable areas (REUA) compared to 10-year-old girls. This reflects the greater sensitivity of their organism to adverse factors. The dominance of the autonomous circuit of regulation was marked for 8- and 10-year-old boys from the RESA. In contrast an imbalance in the operation of regulatory mechanisms with an increase in the central regulatory circuit was found for boys from the REUA. High centralization of cardiac control indicates that adaptation mechanisms are in a state of pronounced tension. The increase in the shift gradient for boys from REUA falls at the age of 10 years. The results of the study revealed gender differences in the regulation of heart rhythm. The obtained data is important diagnostic aspects of morphofunctional maturation of the organism for subsequent ontogenetic stages depending on environmental living conditions.