Previous studies have neglected the first recovery minutes after exercise when studying post-exercise heart rate variability (HRV). The present aim was to evaluate autonomic HR control immediately after exercise using Short-time Fourier transform (STFT) and to compare the effects of low [LI, 29(6)% of maximal power] and high [HI, 61(6)% of maximal power] intensity bicycle exercise on the HRV recovery dynamics. Minute-by-minute values for low (LFP(ln,) 0.04-0.15 Hz) and high (HFP(ln), 0.15-1.0 Hz) frequency power were computed from R-R interval data recorded from 26 healthy subjects during 10 min recovery period after LI and HI. The HRV at the end of exercise and recovery was assessed with Fast Fourier transform as well. The results showed that LFP(ln) and HFP(ln) during the recovery period were affected by exercise intensity, recovery time and their interaction (P < 0.001). HFP(ln) increased during the first recovery minute after LI and through the second recovery minute after HI (P < 0.001). HFP(ln) was higher for LI than HI at the end of the recovery period [6.35 (1.11) vs. 5.12 (1.01) ln (ms(2)), P < 0.001]. LFP(ln) showed parallel results with HFP(ln) during the recovery period. In conclusion, the present results obtained by the STFT method, suggested that fast vagal reactivation occurs after the end of exercise and restoration of autonomic HR control is slower after exercise with greater metabolic demand.