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The effects of short-term high-intensity interval training (HIT) on cardiac autonomic function are unclear. The present study assessed cardiac autonomic adaptations to short-term HIT in comparison with aerobic endurance training (AET).Twenty-six healthy middle-age sedentary men were randomized into HIT (n = 13, 4–6 × 30 s of all-out cycling efforts with 4-min recovery) and AET (n = 13, 40–60 min at 60% of peak workload) groups, performing six sessions within 2 wk. The participants underwent a 24-h ECG recording before and after the intervention and, additionally, recorded R-R interval data in supine position (5 min) at home every morning during the intervention. Mean HR and low-frequency (LF) and high-frequency (HF) power of R-R interval oscillation were analyzed from these recordings.Peak oxygen consumption (V˙O2peak) increased in both groups (P < 0.001). Compared with AET (n = 11), HIT (n = 13) increased 24-h LF power (P = 0.024), tended to increase 24-h HF power (P = 0.068), and increased daytime HF power (P = 0.038). In home-based measurements, supine HF power decreased on the days after HIT (P = 0.006, n = 12) but not AET (P = 0.80, n = 9) session. The acute response of HF power to HIT session did not change during the intervention.In conclusion, HIT was more effective short-term strategy to increase R-R interval variability than aerobic training, most probably by inducing larger increases in cardiac vagal activity. The acute autonomic responses to the single HIT session were not modified by short-term training.