Heart rate variability (HRV) is nowadays based on ECG analysis, mainly as an frequency analysis of heart rate (HR). HR is a parameter of heart reactivity which is used to describe fluctuation of intervals between two consecutive heart beats. The same information about hear function is possible to get from pulse wave measurement which reflects mechanical work of the heart. The paper is focused on the comparison between HRV analysis from standard ECG signal and from pulse wave measurement from different parts of human body. In the paper are described all of methods for signal analysis of ECG and pulse wave measurement. It is also compare the best point from pulse wave to evaluate HR. The aim was to evaluate accuracy of HRV analysis based on the measurement from pulse wave and ECG. Pulse wave measurement is not used in common practise and analyse the changes of HRV during day but it could be more comfortable for the patient.