Our study focuses on a new method of estimating the heart rate variability (HRV) which does not require the use of electrocardiogram (ECG) R-wave detection. Contrary to the R-wave detection method which requires a sampling frequency higher than 100 Hz, the one proposed here can be used to calculate the HRV from an ECG signal sampled at a frequency of approximately 5 Hz with a relative mean error of 0.03. This new method is based on extracting the instantaneous fundamental frequency from the ECG. The method could be efficiently used to extract the HRV from an ECG measured for healthy subjects performing an exercise in which the HRV increases linearly with time, and for subjects with respiratory and cardiac problems. The overall error decreased as we low-pass filtered the HRV with lower cut-off frequencies. Moreover, it was shown that the method could be efficiently used to calculate the HRV from blood pressure measurements and to be robust to noise.