Introduction. The method of processing experimental data obtained in the form of a timevarying non-stationary signal is described. In the experimental study of transients associated with changes in the heart rate of schoolchildren during a proof-reading test, it became necessary to develop a new effective method for processing the results of dynamic measurements. Purpose of the study. Consider the main points of this methodology, which is based on the Prony method, and the possibility of its use in the field of studies of changes in heart rate variability (HRV) in response to various functional test influences. Materials and methods. Traditional approaches related to the calculation of power spectral density (PSD) and based on classical spectral methods are currently very widespread. The model of constant rhythm is not applicable for non-stationary dependencies of HRV. For spectral analysis of time dependences of HRV reflecting transient processes (nonstationary processes) it is proposed to apply spectral analysis on the plane of complex frequencies (PCF). PCF is a generalization of the usual spectrum. The calculation of the PCF is based on the Prony procedure, based on parametric modeling. Results. PCF reflects the frequency structure of oscillations of unsteady physiological signals, therefore, can be used to classify them. It is shown that the use of spectral analysis on the plane of complex frequencies for transient processes of the heart rhythm makes it possible (according to the parameters of the PCF) to calculate, for diagnostic purposes, the numerical values of the parameters characterizing the reactions of various regulatory mechanisms of the heart rhythm in response to various functional test influences. Conclusion. The best results, as compared with the methods of classical spectral analysis, for the analysis of transients in the form of a HRV signal were given by approaches based on the use of spectral analysis on the plane of complex frequencies.