Pulse transit time (PTT) has been reported correlated with heart rate (HR) and blood pressure (BP), however, the results are not consistent in different investigations. Towards a better understanding of the underlying mechanisms of the PTT changes, this study compares the power spectrum density of the variability in PTT with that in HR and BP under rest and post-exercise physiological conditions. Coherence function is also examined to quantify the strength of coupling between paired variabilities. The results show that the pulse transit time variability (PTTV) has significant coherence (>0.5) with heart rate variability (HRV) and blood pressure variability (BPV) under all physiological conditions at high frequency (HF). However, at the low frequency (LF) band, the coherence reduced to insignificance immediately after the exercise (< or =5 minutes after exercise) and then return back to significant level 9 minutes after the exercise. The results show that PTTV is strongly coupled with HRV and BPV at the HF, indicating that the parasympathetic modulation could be the main cause of PTTV. The unstable coupling relationship of PTTV with BPV at LF should raise caution in the beat-to-beat BP estimation by PTT in the dynamic situation.