Heart rate variability (HRV) has long been used in risk stratification for sudden cardiac death and diabetic autonomic neuropathy. In recent years, both time and frequency domain indices of HRV also gained increasing interest in sports and training sciences. In these fields, HRV is currently used for the noninvasive assessment of autonomic changes associated with short-term and long-term endurance exercise training in both leisure sports activity and high-performance training. Furthermore, HRV is being investigated as a diagnostic marker of overreaching and overtraining.A large body of evidence shows that, in healthy subjects and cardiovascular patients of all ages (up to an age of 70 years), regular aerobic training usually results in a significant improvement of overall as well as instantaneous HRV. These changes, which are accompanied by significant reductions in heart rates both at rest and during submaximal exercise, reflect an increase in autonomic efferent activity and a shift in favor of enhanced vagal modulation of the cardiac rhythm. Regular aerobic training of moderate volume and intensity over a minimum period of 3 months seems to be necessary to ensure these effects, which might be associated with a prognostic benefit regarding overall mortality.At present, available data does not allow for final conclusions with respect to the usefulness of traditional HRV indices in assessing an individual's exercise performance and monitoring training load. The discrepant results published so far are due to several factors including insufficient study size and design, and different HRV methods. Large-sized and prospectively designed studies are necessary for clarification. It also remains to be seen, whether the traditional HRV indices prove useful in the diagnosis of overreaching and overtraining. Preliminary results, though promising, need to be confirmed in larger cohorts.A basic problem in HRV analysis is nonstationarity of the heart rate signal, which holds particularly true for exercise conditions. Whether, in these conditions, more robust nonlinear HRV methods offer a benefit has to be established in further work.