BACKGROUND: The aim of the present study was to evaluate the effect of an endurance training program on heart rate variability (HRV) in prepubertal healthy children and to determine the relationships between HRV components and training-induced cardiac adaptations. METHODS: Nineteen prepubertal children (aged 10-11 years old) took part in this study: 12 children were assigned to participate in a 13-week endurance training program (3 x 1 h week-1; intensity, > 80% HRmax) and 7 children served as a control group. Before and after the 13-week study period, all the children were tested for maximal oxygen uptake (V O(2max)), HRV was measured by spectral and time domain analysis of 5 h night ECG recordings, and left ventricular (LV) cardiac morphology and function were assessed by means of Doppler-Echocardiography. RESULTS: V O(2max) increased significantly (+15.5% +/- 12.1; P < 0.01) after the training program. All the frequency domain components (absolute values) increased after training except the low (LF) to high (HF) frequency ratio. Also, LF and HF did not change when expressed relative to total power. For the time domain components, only N-N intervals, the standard deviation of all N-N and the average of all 5 min standard deviations of N-N increased after training. Our training program induced also an increase in LV internal diameter and mass as well as an enhancement in early diastolic passive LV filling with a concomitant reduction in late diastolic active LV filling. These cardiac morphological and functional adaptations did not correlate however, with the autonomous nervous system modifications due to training. CONCLUSION: Our study shows that an endurance training program had a positive effect on aerobic potential, morphological and functional cardiac parameters and on nocturnal global HRV in healthy prepubertal children without inducing sympathetic and parasympathetic modifications.