Autonomic nervous systems have important roles for survival of victims under hypobaric hypoxic condition. In the present study, we assessed the correlation between arterial oxygen saturation (SpO₂) and heart rate variability (HRV) to identify the autonomic nervous responsiveness among trekkers at high altitude (n = 21). HRV was analyzed by the maximum entropy method. SpO₂ among subjects at 3456 m (495 mm Hg) was 80% ± 5% (mean ± SD; range, 69%-93%). SpO₂ and percentile entropy, and SpO₂ and low-frequency variability, had positive correlation (r = 0.455 and 0.518, respectively). SpO₂ value among subjects with mountain sickness symptoms was not different from that among subjects without the symptoms. In conclusion, autonomic responses among high-altitude trekkers may be blunted under hypobaric hypoxic conditions. Deterioration of autonomic function measured by HRV might be more sensitive to hypoxia than clinical symptoms at high altitudes.