This study evaluated the effect of pulse arrival time (PAT) on the difference between heart rate variability (HRV) and pulse rate variability (PRV). HRV is the degree of fluctuation in the time intervals between heart beats obtained from ECG, and is a global measure of autonomic nervous system (ANS) function. PRV is obtained from photoplethysmogram (PPG), and several researchers have attempted to use PRV instead of HRV for ANS monitoring, because measuring PPG is easier than measuring ECG. PPG reflects the change in blood volume ejected from the heart. Therefore, there is a strong correlation between the HRV and the PRV, and the PRV is regarded as an acceptable alternative to HRV at rest in ANS evaluation. In this study, we focused on the influence of change of body position on PRV, and we evaluated the effect of PAT on the difference between HRV and PRV. PAT is the sum of pulse transit time (PTT) and the pre-ejection period. Therefore, we used PAT to verify the difference between HRV and PRV. Seven healthy volunteers participated in this experiment. Their ECG and PPG were simultaneously recorded for 5 min before and 5 min after standing up from a chair. The results of the correlation coefficient indicated a strong correlation (r=0.9) between the HRV and the PRV in both sitting and standing positions. In contrast, the results of high-frequency spectral component showed a significant difference while standing, suggesting the influence of PAT on PRV. These results indicate that PRV is not identical to HRV, and that we should pay attention to use PRV instead of HRV for measuring ANS function.