Due to the widespread use and simplicity of photoplethysmography (PPG) signals, and because this signal contains information related to pulse rate, several studies have started to propose the use of Pulse Rate Variability (PRV) for the assessment of cardiovascular autonomic nervous activity, instead of using Heart Rate Variability (HRV) obtained with the electrocardiogram (ECG). However, there is a lack of standardisation and guidelines for the measurement of PRV from PPG signals, which might hinder comparability among studies and validation of results. The aim of this study was to evaluate different digital filters on PPG signals and their effects on PRV information, compared to HRV obtained from ECG. PPG and ECG signals obtained from healthy volunteers were used to measure HRV and PRV. PPG signals were filtered using different FIR and IIR digital filters, with several cut-off frequencies. The results indicate that filtering PPG signals using IIR filters and lower low-cut-off frequencies allow for the acquisition of more reliable PRV information, with lower Bland-Altman ratios and higher cross-correlations when compared to HRV. This is a first step in establishing guidelines and standards for the analysis of PRV information using PPG signals.Clinical relevance- Pulse rate variability might be a useful tool for the assessment of the cardiovascular autonomic nervous system. This study is the first step for establishing standards of measurement of this signal, which helps in the comparability and validation of the technique.