Aim of the study was to compare the ANS functioning, as measured by heart rate variability (HRV), in athletes with non-functional overreaching (NFO) and overtraining syndrome (OTS) and in athletes without NFO/OTS. In 43 athletes with NFO/OTS, 40 athletes without NFO/OTS, as well as in 35 sedentary subjects the ANS function was evaluated with the Autonomic Balance Test, based on the HRV analysis of resting heart rate recordings. Results of the study show lower HRV and lower vagal influence along with increased sympathetic cardiovascular control in athletes with non-functional overreaching and particularly in athletes with overtraining, than in highly trained athletes without NFO/OTS. "Stress Response" in athletes with NFO, as well as in some athletes with OTS, showing sympathetic dominance, considered as a sign of physical or mental fatigue and chronic stress, whereas "Total Autonomic Dystonia" in most of the athletes with OTS (67%) reflects more advanced stage of maladaptation associated with depressed regulatory function of the ANS, both sympathetic, as well as vagal influences. Most frequently NFO and OTS were seen in wrestling, which needs further investigation and regular medical monitoring. Thus, results of the study show progression of autonomic imbalance and depression of regulatory function of the autonomic nervous system in athletes with OTS. The cardiac autonomic imbalance observed in overtrained athletes implies changes in HRV and therefore would consider that heart rate variability may provide useful information in detection of overtraining in athletes and can be a valuable adjacent tool for optimising athlete's training program as well as for timely diagnosis and prevention of progression of NFO/OTS.