The effect of intermittent normobaric hypoxia (INH) of sanogenic level on children living in radioactively contaminated territories has been investigated. Children divided into three groups: 37 patients were included in the main group (the 1st group – medical therapy according to the protocols and INH sessions), 35 persons – in the comparison group (the 2nd group – medical therapy), 30 persons – in the control group (the 3rd group – healthy persons). A significant increase in RMSSD index by 36% in phone registration was established in children aged 6-11 years of the main group after combined treatment with INH sessions (10-12% oxygen in nitrogen), and by 27% under the use of orthoclinostatic test in children aged 12-17 years. A decrease of the sympathovagal index by 23 % in children aged 6-11 years was demonstrated concerning the group of comparison. The tension index of regulatory systems was decreased in children of both groups, that is indicative of the decrease in the central contour of cardiac rhythm control.