PURPOSE: The purpose of this study is to establish the alterations in the activity of the autonomic nervous system (ANS) via heart rate variability (HRV) in subjects exposed to 1 h of exogenous hypoxia for 10 consecutive days. METHODS: Twelve healthy non-smoker males at mean age of 29.8 +/- 7.4 (mean +/- SD) breathed hypoxic air delivered through hypoxicator (Ficapital O, Cyrillic(2) = 12.3% +/- 1.5%) for 1 h in 10 consecutive days. Pulse oximetry and electrocardiography were monitored during the visit and HRV was calculated for the entire 1-h hypoxic period. RESULTS: Comparing the last hypoxic visit to the first, subjects had higher standard deviation of normal-to-normal interbeat intervals (SDNNs) (65.7 +/- 32.5 vs. 81.1 +/- 32.0 ms, p = 0.013) and root mean square of successive R-R interval difference (RMSSD) (58.1 +/- 30.9 vs. 76.5 +/- 34.6 ms, p = 0.029) as well as higher lnTotal power (8.1 +/- 1.1 vs. 8.5 +/- 0.9 ms(2), p = 0.015) and high frequency (lnHF) (6.8 +/- 1.3 vs. 7.5 +/- 1.2 ms(2), p = 0.05) and lower LF/HF (2.4 +/- 1.4 vs. 1.5 +/- 1.0, p = 0.026). Changes in saturation (87.0 +/- 7.1 vs. 90.8 +/- 5.0%, p = 0.039) and heart rate (67.1 +/- 8.9 vs. 62.5 +/- 6.0 beats/min, p = 0.040) were also observed. CONCLUSIONS: Intermittent hypoxic training consisting of 1-h hypoxic exposure for 10 consecutive days could diminish the effects of acute exogenous hypoxia on the ANS characterized by an increased autonomic control (SDNN and total power) with augmentation of the parasympathetic nervous system activity (increased RMSSD and HF and decreased LF/HF). Therefore, it could be applied as a pre-acclimatization technique aiming at an increase in the autonomic control and oxygen saturation in subjects with upcoming sojourn to high altitude.