HRV and HRT are independent predictors of cardiovascular mortality. Aging reduces HRV, but results from the physical exercise trials are controversial. The primary aim was to study changes in heart rate variability (HRV) and heart rate turbulence (HRT) in a six-year controlled randomized trial at regular low to moderate intensity physical exercise. One hundred forty men aged 53--63 years were randomized in to an exercise or a control groups. The participants underwent a maximal bicycle ergometer exercise test with respiratory gas analyses annually for six years. At baseline and after intervention, 24-h ambulatory ECG registrations were performed to assess HRV (n=100). HRT was determined among subjects with single ventricular premature complexes (VPC) (n=73). In the exercise group, ventilatory aerobic threshold (VAT) increased by 16% indicating enhanced submaximal cardiorespiratory fitness. No significant differences were found in any of the HRV or HRT parameters between the groups. However, the observed increase in VAT correlated significantly with the improvement in HRV parameters. The change in turbulence slope (TS) correlated with the changes in most HRV variables and the change in turbulence onset (TO) correlated with the changes in three frequency domain parameters. Our results suggest that in addition to improvement in submaximal cardiorespiratory fitness, regular low to moderate intensity physical exercise seems to have beneficial effects also on cardiac autonomic nervous function, a clinically relevant predictor of cardiovascular morbidity and mortality.