This study aimed to analyze measures of heart rate variability (HRV) to provide reference values in Ultra-Trail Running (UTR) athletes. Sixteen Chilean UTR were monitored with 5-minute baseline wake-up records during a one-year follow-up during which they maintained their usual training, competition and rest activities. As a variable to evaluate parasympathetic activity the RMSSD (square root of the mean value of the sum of the squared differences of all successive RR intervals) was analyzed. In addition, the Stress Score (SS) was calculated as an indicator of sympathetic activity. The data provided are reference baseline HRV values for UTR through a percentile distribution, which can be particularly useful when HRV is used to control training loads in UTR athletes.