The autonomic nervous system controls the smooth muscles of the internal organs, the cardiovascular system and the secretory function of the glands and plays a major role in the processes of adaptation. Heart rate variability is a non-invasive and easily applicable method for the assessment of its activity. The following review describes the origin, parameters and characteristics of this method and its potential for evaluation of the changes of the autonomic nervous system activity in different physiological and pathological conditions such as exogenous hypoxia, physical exercise and sleep. The application of heart rate variability in daily clinical practice would be beneficial for the diagnostics, the outcome prognosis and the assessment of the effect of treatment in various diseases.