Background: Heart rate variability (HRV) as a measure of the cardiac autonomic nervous system activity (CANA) has the potential to tailor endurance training and may contribute to the prevention of overtraining. We aimed to investigate whether there are sex differences and sex-specific reactions of the CANA to different training periods (TPs) in Swiss elite runners. Methods: Two HRV measurements (each 5 minutes supine and 5 minutes standing) per athlete were performed, the first during preparation period (PP) and the second during competition period (CP).