The aims of the present study were to (1) assess relationships between running performance and parasympathetic function both at rest and following exercise, and (2) examine changes in heart rate (HR)-derived indices throughout an 8-week period training program in runners. In 14 moderately trained runners (36 +/- 7 years), resting vagal-related HR variability (HRV) indices were measured daily, while exercise HR and post-exercise HR recovery (HRR) and HRV indices were measured fortnightly. Maximal aerobic speed (MAS) and 10 km running performance were assessed before and after the training intervention. Correlations (r > 0.60, P < 0.01) were observed between changes in vagal-related indices and changes in MAS and 10 km running time. Exercise HR decreased progressively during the training period (P < 0.01). In the 11 subjects who lowered their 10 km running time >0.5% (responders), resting vagal-related indices showed a progressively increasing trend (time effect P = 0.03) and qualitative indications of possibly and likely higher values during week 7 [+7% (90% CI -3.7;17.0)] and week 9 [+10% (90% CI -1.5;23)] compared with pre-training values, respectively. Post-exercise HRV showed similar changes, despite less pronounced between-group differences. HRR showed a relatively early possible decrease at week 3 [-20% (90% CI -42;10)], with only slight reductions near the end of the program. The results illustrate the potential of resting, exercise and post-exercise HR measurements for both assessing and predicting the impact of aerobic training on endurance running performance.