Studies of heart rate variability (HRV) have so far produced contradictory evidence to support the common belief that endurance training enhances cardiac parasympathetic tone. This may be related to the fact that most studies failed to specifically isolate the vagally mediated influence of respiration. This study used a cross-sectional comparison of endurance athletes (n=20; ATHL) exhibiting resting bradycardia and age-matched nonathletes (n=12; CRTL) to indirectly assess training effects on amplitude and timing characteristics of respiratory sinus arrhythmia (RSA). Continuous electrocardiogram (ECG) and ventilatory flows were recorded during spontaneous breathing (SP), as well as during breathing at four cycles less than (M4) or more (P4) than SP, to also examine potential repercussions of training on the sensitivity of the cardiac vagal responses to breathing. A fast Fourier transform procedure was used to quantify the standard spectral high-frequency (HF) and low-frequency (LF) components and a respiratory-centered frequency (RCF) component of HRV. RSA was assessed using a breath-by-breath quantification of the amplitude and timing of the maximum change in instantaneous heart rate. Under baseline SP conditions, heart rate was lower in ATHL (62.6+/-6.5 vs. 75.2+/-9 beats/min; p<0.05) while blood pressure (BP), breath cycle duration, tidal volume, and ventilatory drive were similar in both groups. HRV total spectral power density, LF, HF, or RCF was not different between groups at either the SP, M4, or P4 conditions. Changes in total breath duration similarly affected RSA amplitude in all groups, while HR and BP remained unchanged from SP. RSA phase was not affected by training status or by changes in total breath duration. RSA amplitude was negatively related to breathing frequency in all groups (p<0.05), while the mean slope of the relationship (sensitivity) was not different between groups. In as much as RSA is an adequate marker of cardiac vagal efferent activity, these results add support to a contribution of a decrease in intrinsic heart rate to explain training-induced bradycardia.