The article presents the main provisions of the methodology for the analysis of heart rate variability (HRV), which is now actively and widely implemented in many fields of medicine and applied physiology. This methodology was first developed in space medicine, where, already during the first manned spaceflights, there was a need in operative assessment of the person's reactions and abilities to maintain high performance and good level of health under different stress conditions.The HRV analysis methodology is based on the measurement of a consecutive series of cardiac cycle durations, for which electrocardiography, rheocardiography, ballistic cardiography, etc., can be used. The resulting numerical series are subjected to mathematical analysis using statistical, spectral and other methods. The results are interpreted as medical and physiological criteria of the functional state of the organism.Based on the mathematical model, a probabilistic approach to the prediction of pathological conditions was proposed. Indicators of the stress degree of regulatory systems and their functional reserve, which are calculated from the HRV analysis data, are used in the mathematical model of the functional states. In order to obtain the decision rules for the recognition of identified classes of functional states the stepwise discriminant analysis has been applied.Equations of the discriminant function were obtained. This article examines in detail this new probabilistic approach to the HRV analysis and provides examples of its use for assessing the functional state of cosmonauts at various stages of long space flights.