Physiological variation of the interval between consecutive heartbeats is known as the heart rate variability (HRV). HRV analysis is traditionally performed on electrocardiograms (ECG signals) and has become a useful tool in the diagnosis of different clinical and functional conditions. The progress in the sensor technique encouraged the development of alternative methods of analyzing cardiac activity: Seismocardiography and gyrocardiography. In our study we performed HRV analysis on ECG, seismocardiograms (SCG signals) and gyrocardiograms (GCG signals) using the PhysioNet Cardiovascular Toolbox. The heartbeats in ECG were detected using the Pan–Tompkins algorithm and the heartbeats in SCG and GCG signals were detected as peaks within 100 ms from the occurrence of the ECG R waves. The results of time domain, frequency domain and nonlinear HRV analysis on ECG, SCG and GCG signals are similar and this phenomenon is confirmed by very strong linear correlation of HRV indices. The differences between HRV indices obtained on ECG and SCG and on ECG and GCG were statistically insignificant and encourage using SCG or GCG for HRV estimation. Our results of HRV analysis confirm stronger correlation of HRV indices computed on ECG and GCG signals than on ECG and SCG signals because of greater tolerance to inter-subject variability and disturbances.