In the article the beneficial effects of individually adjusted single interval hypoxic hypercapnic session (IHHS) on parameters of heart rate variability (HRV) and of aerobic metabolism are demonstrated and interactions between studied indexes are discussed. In 24 athletes, hypoxia was achieved in closed breathing circuit under constant pulseoxymetry control. Before and after IHHS short time HRV recordings were performed and activity of catalase, superoxidedesmutase (SOD), thiobarbituric acid reactive species (TBARS), oxidative modification products, middle mass molecules and ligand forms of hemoglobin (Hb) were assessed. The results showed an increase in total spectral power and parasympathetic activity with simultaneous decrease in sympathetic component in all athletes. These changes resulted from activation of aerobic metabolism, because the most prominent improvement of HRV parameters was observed in athletes with decrease in TBARS without major changes of catalase and SOD activities after IHHS. The radical nature of activation in this group was further confirmed by redistribution of ligand forms of Hb (IHbO2, -MetHb, -HbCO, -HbS). The role of hermoproteins in regulation of free radical reactions is discussed. It has been demonstrated that individually adjusted IHHS regimen can improve HRV parameters by training the mechanisms of endogenous oxygen production and efficient modulation of different impulses from chemoreceptors. Partially, such result may be attributed to monitoring of SaO2 during IHHS, which adequately reflects the organism ability to produce metabolic oxygen.