INTRODUCTION: Measures of HR variability (HRV) have shown potential to be of use in training prescription. PURPOSE: The aim of this study was to investigate the effectiveness of using HRV in endurance training prescription. METHODS: Forty recreational endurance runners were divided into the HRV-guided experimental training group (EXP) and traditional predefined training group (TRAD). After a 4-wk preparation training period, TRAD trained according to a predefined training program including two to three moderate- (MOD) and high-intensity training (HIT) sessions per week during an 8-wk intensive training period. The timing of MOD and HIT sessions in EXP was based on HRV, measured every morning. The MOD/HIT session was programmed if HRV was within an individually determined smallest worthwhile change. Otherwise, low-intensity training was performed. Maximal oxygen consumption (V O2max) and 3000-m running performance (RS3000m) were measured before and after both training periods. RESULTS: The number of MOD and HIT sessions was significantly lower (P = 0.021, effect size = 0.98) in EXP (13.2 +/- 6.0 sessions) compared with TRAD (17.7 +/- 2.5 sessions). No other differences in training were found between the groups. RS3000m improved in EXP (2.1% +/- 2.0%, P = 0.004) but not in TRAD (1.1% +/- 2.7%, P = 0.118) during the intensive training period. A small between-group difference (effect size = 0.42) was found in the change in RS3000m. V O2max improved in both groups (EXP: 3.7% +/- 4.6%, P = 0.027; TRAD: 5.0% +/- 5.2%, P = 0.002). CONCLUSION: The results of the present study suggest the potential of resting HRV to prescribe endurance training by individualizing the timing of vigorous training sessions.