The aim of this study was to investigate factors that can predict individual adaptation to high-volume or high-intensity endurance training. After the first 8-week preparation period, 37 recreational endurance runners were matched into the high-volume training group (HVT) and high-intensity training group (HIT). During the next 8-week training period, HVT increased their running training volume and HIT increased training intensity. Endurance performance characteristics, heart rate variability (HRV), and serum hormone concentrations were measured before and after the training periods. While HIT improved peak treadmill running speed (RSpeak) 3.1 ± 2.8% (P< 0.001), no significant changes occurred in HVT (RSpeak: 0.5 ± 1.9%). However, large individual variation was found in the changes of RSpeak in both groups (HVT: −2.8 to 4.1%; HIT: 0–10.2%). A negative relationship was observed between baseline high-frequency power of HRV (HFPnight) and the individual changes of RSpeak (r= −0.74,P= 0.006) in HVT and a positive relationship (r= 0.63,P= 0.039) in HIT. Individuals with lower HFP showed greater change of RSpeak in HVT, while individuals with higher HFP responded well in HIT. It is concluded that nocturnal HRV can be used to individualize endurance training in recreational runners.