PURPOSE: To analyze the training structure following a heart rate variability (HRV) -guided training or traditional training protocol, determining their effects on the cardiovascular performance of professional endurance runners, and describing the vagal modulation interaction. METHODS: This was an 8-week cluster-randomized controlled trial. Twelve professional endurance runners were randomly assigned to an HRV-guided training group (HRV-G; n = 6) or a traditional training group (TRAD-G; n = 6). The training methodology followed by the HRV-G was determined by their daily HRV scores. Training intensities were recorded daily. HRV4Training was used to register the rMSSD every morning and during a 60-second period. Cardiovascular outcomes were obtained through an incremental treadmill test. The primary outcome was the maximal oxygen uptake (VO(2max)). RESULTS: Total training volume was significantly higher in TRAD-G, but moderate intensity training was significantly higher in HRV-G (X +/- SD(Dif)=1.98 +/- 0.1%; P = 0.006; d = 1.22) and low intensity training in TRAD-G (X +/- SD(Dif)=2.03 +/- 0.74%; P = 0.004; d = 1.36). The maximal velocity increased significantly in HRV-G (P = 0.027, d = 0.66), while the respiratory exchange ratio increased in TRAD-G (P = 0.017, d = 1). There was a small effect on the LnRMSSD increment (P = 0.365, d = 0.4) in HRV-G. There were statistical inter-group differences in the 鈭唌aximal heart rate when 鈭哃nrMSSD was considered as a covariable (F = 7.58; P = 0.025; d = 0.487). There were significant and indirect correlations of LnRMSSD(TEST) with VO(2max) (r =-0.656, P = 0.02), 鈭哃nrMSSD with 鈭哣O(2max) (r = -0.606, P = 0.037), and 鈭哃nrMSSD(CV) with 鈭哣ENT (r = -0.790, P = 0.002). CONCLUSIONS: higher HRV scores suggest better cardiovascular adaptations due to higher training intensities, favoring HRV as a measure to optimize individualized training in professional runners.