Eleven previously sedentary adult males, serving as the experimental (EXP) group [mean (SE) age 36.6 (1.7) years, body mass 87.2 (4.3) kg, body mass index, BMI, 28.4 (1.5) kgm(-2)] participated in a 16-week supervised exercise program (3 days x week(-1), 30 min day(-1), at approximately equal to 80% of heart rate reserve) to determine the temporal effects of a moderate-to-vigorous-intensity exercise program on heart rate variability (HRV). Five sedentary males [mean (SD) age 36.6 (4.2 )years, body mass 83.8 (6.6) kg, BMI 22.8 (1.7) kg x m(-2)] served as non-exercising controls (CON). HRV was measured every 4 weeks from a resting electrocardiogram obtained while subjects paced their breathing at 10 breaths x min(-1) (0.167 Hz). The time-domain measures of HRV recorded were the proportion of adjacent intervals differing by more than 50 ms (pNN50), the root mean square of successive differences (rMSSD), and the standard deviation of the resting interbeat interval. The frequency-domain measures recorded were high (HF) and low (LF) frequency oscillations, as determined using the fast Fourier transform technique. Aerobic capacity (i.e., peak oxygen uptake) increased by 13.8% in EXP (P < 0.001), but did not change in CON. Resting heart rate did not change in either EXP or CON. In EXP, pNN50 at week 12 (P<0.01), rMSSD at weeks 12 (P < 0.01) and 16 (P = 0.05), and HF power at weeks 12 (P < 0.01) and 16 (P = 0.05) were elevated above baseline. Time- and frequency-domain measures of HRV remained unchanged in CON. It is concluded that a moderate-to-vigorous-intensity exercise program produces increases in time- and frequency-domain measures of HRV within 12 weeks.