The purpose of this study was to assess the adaptive effects of endurance training on autonomic functions in athletes with spectral analysis of cardiovascular variability signals. Continuous ECG, arterial blood pressure (ABP), and respiratory signals were recorded from 15 athletes (VO2max > 55 ml/(kg.min)) and 15 nonathletes (VO2max < 45 ml/(kg.min)) in the sitting position during controlled respiration (tidal volume 700 ml and 15 cycles/min). The autonomic functions were assessed by the normalized low-frequency power (LF power: 0.06-0.14 Hz) and high-frequency power (HF power: the region of the respiratory frequency based on respiratory spectrum) obtained from the autospectra of the RR interval, systolic arterial pressure (SAP), and diastolic arterial pressure (DAP) variability signals. The spontaneous baroreflex sensitivity (BRS) was evaluated by the moduli, BRSLF and BRSHF, of the transfer function between the RR interval and SAP variability in LF and HF bands. The resting HR in athletes was significantly lower than that in nonathletes. In the case of RR interval spectra, the HF power was significantly higher in athletes than in nonathletes, whereas the LF power was significantly lower in athletes than in nonahtletes. These differences might reflect an alteration of sympathovagal interaction with a predominance of parasympathetic activity. However, there was no significant difference in the LF power of SAP and DAP autospectra, reflecting the sympathetic vascular control. The BRSLF and BRSHF were significantly higher in athletes as compared with nonathletes. These results indicate that endurance training induces autonomic imbalance (i.e., the enhanced vagal activities/the attenuated sympathetic tone), which may in part contribute to the resting bradycardia and an increase in the spontaneous BRS in athletes.