The aim of the study was to investigate the influence of training load and exercise mode on heart rate variability and heart rate recovery (HRR) in healthy individuals. The subjects were divided into three groups: sedentary (SED), resistance trained (RT) and aerobically trained (RT). Resting and postmaximal exercise RR intervals were recorded on supine and seated position, respectively. The HRV indices calculated in the resting position were RMSSD and LF and HF power densities. The following HRR indices were calculated throughout the 5-minute postmaximal recovery period: semi-logarithmic regression analysis of the first 30 s (T30); absolute difference between the peak and 60 s HR (HRR(60s)); and mono-exponential time constant of HRR (HRRtau). The RMSSD on subsequent 30-s segments (RMSSD(30s)) on recovery period was also calculated. Both RT and AT groups presented faster HRR than SED (P<0.05). The aerobic trained group was the only group that presented vagal reactivation, when analysing the RMSSD(30s). There were no correlations between the Baecke sport score and the HRV vagal-related indices. However, it was significantly correlated with HRR. It was concluded that that the training load positively influences the HRR, but has no effect on the HRV at rest and that the type of exercise, showed a marked influence on HRV recovery.