The autonomic nervous system dynamically controls the response of the body to a range of external and internal stimuli, providing physiological stability in the individual. With the progress of information technology, it is now possible to explore the functioning of this system reliably and non-invasively using comprehensive and functional analysis of heart rate variability. This method is already an established tool in cardiology research, and is increasingly being used for a range of clinical applications. This review describes the theoretical basis and practical applications for this emerging technique.