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Measures of HR variability (HRV) have shown potential to be of use in training prescription.The aim of this study was to investigate the effectiveness of using HRV in endurance training prescription.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.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).The results of the present study suggest the potential of resting HRV to prescribe endurance training by individualizing the timing of vigorous training sessions.