Abstract. Background: early recognition of hypoxia may decrease aviation accidents happening due to human error and measurement of heart rate variability can be a tool to detect hypoxic events. We aim to determine if heart rate variability relates to hypoxia exposure in subjects who carried out hypobaric chamber training. Methods: we studied 44 pilots during hypobaric hypoxia. Oxygen saturation, time of exposure to hypoxia and heart rate variability were measured in the three phases of flight: denitrogenation, hypoxia and descent to ground and analyzed through an autoregressive model, and a fast fourier transform for high frequency, low frequency and the low frequency/high frequency ratio. Results: population was composed of 44 Colombian Air Force male pilots, 42 males and 2 females, between the ages of 20 and 40, with a median age of 27.5 years. The power of high frequency and low frequency decreased from denitrogenation to hypoxia and increased from hypoxia to descent to ground. The low frequency/high frequency ratio increased during the whole experiment in fast fourier transform. The autoregressive model failed to show statistical significance for high frequency from hypoxia to descent to ground and for the low frequency/high frequency ratio from denitrogenation to hypoxia. Conclusion: hypoxia leads to changes in the autonomous nervous system balance that can be assessed through heart rate variability. More studies are needed to quantify the impact of heart rate variability on decision-making ability and accident prevention in the aviation field.