The mathematical analysis and the assessment of heart rate variability (HRV) based on computer systems can assist the diagnostic process with determining the cardiac status of patients. The new cardio-diagnostic assisting computer system created uses the classic Time-Domain, Frequency-Domain, and Time-Frequency analysis indices, as well as the nonlinear methods (Poincare plot, Recurrence plot, Hurst R/S method, Detrended Fluctuation Analysis (DFA), Multi-Fractal DFA, Approximate Entropy and Sample Entropy). To test the feasibility of the software developed, 24-hour Holter recordings of four groups of people were analysed: healthy subjects and patients with arrhythmia, heart failure and syncope. Time-Domain (SDNN < 50 ms, SDANN < 100 ms, RMSSD < 17 ms) and Frequency-Domain (the spectrum of HRV in the LF < 550 ms(2), and HF < 540 ms(2)) parameter values decreased in the cardiovascular disease groups compared to the control group as a result of lower HRV due to decreased parasympathetic and increased sympathetic activity. The results of the nonlinear analysis showed low values of (SD1 < 56 ms, SD2 < 110 ms) at Poincare plot (Alpha < 90 ms) at DFA in patients with diseases.Significantly reducing these parameters are markers of cardiac dysfunction. The examined groups of patients showed an increase in the parameters (DET% > 95, REC% > 38, ENTR > 3.2) at the Recurrence plot. This is evidence of a pathological change in the regulation of heart rhythm. The system created can be useful in making the diagnosis by the cardiologist and in bringing greater accuracy and objectivity to the treatment.