The expansion of heart rate variability analysis has been facilitated by the remarkable development of computer sciences and digital signal processing during the last thirty years. The beat-to-beat fluctuation of the heart rate originates from the momentary summing of sympathetic and parasympathetic influences on the sinus node. According to the extensive associations of the autonomic nervous system, several factors affect heart rate and its variability such as posture, respiration frequency, age, gender, physical or mental load, pain, numerous disease conditions, and different drugs. Heart rate variability can be quantitatively measured by time domain and frequency domain methods that are detailed in the paper. Non-linear methods have not spread in the clinical practice yet. Various cardiovascular and other pathologies as well as different forms of mental and physical load are associated with altered heart rate variability offering the possibility of predicting disease outcome and assessing stress.