Daily aerobic training results in autonomic control of the heart toward vagal dominance. The constancy of vagal dominance after controlled training followed by a home-based training program in accordance with contemporary guidelines is not known. We set out here to study whether the vagal dominance induced by 8 weeks of controlled aerobic training is preserved after a 10-month home-based training program. For the controlled study, healthy men were randomized as training (n=18) and control subjects (n=6). The training was started by a supervised 8-week period with six training sessions a week [45 (15) min each] at an intensity of 70-80% of maximum heart rate, followed by a home-based training program for 10 months in accordance with the American College of Sports Medicine recommendations. Cardiovascular autonomic function was assessed by analyzing HR variability over a 24-h period and separately during the night hours (midnight-6 a.m.). Maximal running performance improved during the controlled training 16 (7)% (range 4-31%, P<0.001) and remained 8 (8)% (range -3 to 23%, P<0.001) above the baseline level after the home-based training program. At night, the vagally mediated high-frequency (HF) power of R-R intervals increased during the controlled training from 6.7 (1.3) to 7.3 (1.1) ln ms2 ( P<0.001) and remained higher than the baseline after the home-based training [7.0 (1.3) ln ms2, P<0.05]. The changes in running performance correlated with the changes in HF power at night (r=0.41, P<0.05) and over 24 h (r=0.44, P<0.05) after the home-based training program. Similarly, the changes in body mass index correlated with the changes in HF power over 24 h (r=-0.44, P<0.05) after the home-based training program. The high vagal outflow to the heart after the home-based training is associated with good physical performance and body mass control.