Purpose:To assess the effect of supramaximal intermittent exercise on long-term cardiac autonomic activity, inferred from heart rate variability (HRV).Methods:Eleven healthy males performed a series of two consecutive intermittent 15-s runs at 95% VIFT (i.e., speed reached at the end of the 30-15 Intermittent Fitness Test) interspersed with 15 s of active recovery at 45% VIFT until exhaustion. Beat-to-beat intervals were recorded during two consecutive nights (habituation night and 1st night) before, 10 min before and immediately after exercise, as well as 12 h (2nd night) and 36 h (3rd night) after supramaximal intermittent exercise. The HRV indices were calculated from the last 5 min of resting and recovery periods, and the first 10 min of the first estimated slow wave sleep period.Results:Immediate post-supramaximal exercise vagal-related HRV indices were significantly lower than immediate pre-supramaximal exercise values (P < .001). Most vagal-related indices were lower during the 2nd night compared with the 1st night (eg, mean RR intervals, P = .03). Compared with the 2nd night, vagal-related HRV indices were significantly higher during the 3rd night. Variables were not different between the 1st and 3rd nights; however, we noted a tendency (adjusted effect size, aES) for an increased normalized high-frequency component (P = .06 and aES = 0.70) and a tendency toward a decreased low-frequency component (P = .06 and aES = 0.74).Conclusion:Results confirm the strong influence of exercise intensity on short- and long-term post exercise heart rate variability recovery and might help explain the high efficiency of supramaximal training for enhancing indices of cardiorespiratory fitness.