PURPOSE: To test the utility of HR variability (HRV) in daily exercise prescription in moderately active (approximately two exercises per week) men and women. METHODS: A total of 21 men and 32 women were divided into standard training (ST: males = 7 and females = 7), HRV-guided training (HRV-I: males = 7 and females = 7; HRV-II: females = 10), and control (males = 7 and females = 8) groups. The 8-wk aerobic training period included 40-min exercises at moderate and vigorous intensities (70% and 85% of maximal HR). The ST group was instructed to perform two or more sessions at moderate and three or more sessions at vigorous intensity weekly. HRV-I and HRV-II groups trained on the basis of changes in HRV, measured every morning. In the HRV-I group, an increase or no change in HRV resulted in vigorous-intensity training on that day. Moderate-intensity exercise or rest was prescribed if HRV had decreased. The HRV-II group performed a vigorous-intensity exercise only when HRV had increased. Peak oxygen consumption (VO2peak) and maximal workload (Loadmax) were measured by a maximal bicycle ergometer test before and after the intervention. RESULTS: The changes in VO2peak did not differ between the training groups either in men or in women. In men, the change in Loadmax was higher in the HRV-I group than in the ST group (30 +/- 8 vs 18 +/- 10 W, P = 0.033). In women, no differences were found in the changes in Loadmax between the training groups (18 +/- 10, 15 +/- 11, and 18 +/- 5 W for ST, HRV-I, and HRV-II, respectively). The HRV-II group performed fewer vigorous-intensity exercises than the ST and HRV-I groups (1.8 +/- 0.3 vs 2.8 +/- 0.6 and 3.3 +/- 0.2 times per week, respectively, P < 0.01 for both). CONCLUSIONS: HRV measurements are beneficial in exercise training prescription in moderately active men and women. Women benefit from HRV guidance by achieving significant improvement in fitness with a lower training load.