Objectives: Elderly passengers and those with preexisting disease are flying with increasing frequency and in-flight cardiac emergencies are a more frequent occurrence. We conducted a study of the physiological effects of simulated cabin altitudes and resulting lower oxygen levels among such passengers.Methods: We monitored 41 participants in a hypobaric chamber for 2 days, one at an equivalent of 7,000 feet altitude (regulations limit pressurization to 8,000 feet) for a 4–5 h simulated flight and the other at ground level using generalized least squares models to account for repeated measures. We evaluated associations between simulated flight, heart rate (HR) and measures of heart rate variability(HRV) (root mean square of successive R-R interval differences [RMSSD], standard deviation of normal-to-normal intervals [SDNN], high-frequency power [HF], and low-frequency power [LF]).Results: Heart rate was 3.9% (95% CI: 2.1, 5.8) higher on simulated flight days compared with non-flight days. The RMSSD was 10.6% (95% CI: −21.3, 0.05) lower during simulated flight days, indicative of reduced HRV. The remaining HRV measures were also lower on simulated flight days, though associations were less precise.Conclusion: We report that typical simulated flight conditions elicit changes in cardiac autonomic control, suggesting sympathetic arousal or reductions in parasympathetic drive. Our findings, if confirmed, may suggest the need for guidelines to protect vulnerable passengers including prescreens, symptom evaluation after air travel, the use of oxygen concentrators, and education about healthy behaviors in flight.