Methodological problems have limited the number of studies on heart rate variability (HRV) dynamics immediately after exercise. We used the short-time Fourier transform method to study immediate (5 min) and slow (30 min) recovery of HRV after different high-intensity exercise interventions. Eight male athletes performed two interval interventions at 85% and 93% (IV(85) and IV(93)) and two continuous interventions at 80% and 85% (CO(80) and CO(85)) of the velocity at VO2max (vVO2max). We found no increase in high frequency power (HFP), but low frequency (LFP) and total power (TP) increased (P<0.05) during the first 5 min of the recovery after each intervention. During the 30-min recovery, HFP, LFP and TP (1) increased slowly toward resting values, but HFP remained lower (P<0.01) than at rest, (2) were lower (P<0.05) after IV(93) and CO(85) when compared with IV(85) and CO(80), respectively and (3) were lower (P<0.01) after CO(85) when compared with IV(85). HRV recovery was detected during the immediate recovery after interventions. Increased exercise intensity resulted in lower HRV both in interval and in continuous interventions. In addition, when interval and continuous interventions were performed at a similar workload, HRV was lower after continuous intervention.