The R-peak localization error (jitter) of a heart rate variability (HRV) system has a great impact on the values of the HRV measures. Only a few studies have analyzed this subject and purely done so from the aspect of choice of sampling frequency. In this study we provide an overview of the various factors that comprise the jitter of a system. We propose a method inspired by the field of signal averaged electrocardiography (SAECG) that allows for a quantification of the jitter of any HRV system that records and stores the raw ECG signal. Furthermore, with this method the differences between the HRV measures of the system and HRV measures corresponding to the physiological truth can be quantified. The method is used to obtain the physiologically true R-peak locations of subjects from Physionet's 'Normal Sinus Rhythm Database'. The effects of jitter are then analyzed via mathematical modelling for short-term and long-term HRV for various HRV measures. The effects of abnormal beats and missed and false detections are analyzed as well.