The purpose of this study is to measure the temporary intervals between R peak with ECG and pulse peak with photoplethysmography (PPG) and then to compare their precisions of two types of heart rate variability (HRV) analyses, power spectral analysis and Tone-Entropy analysis. A lot of papers used to measure cardiac autonomic nervous system (CANS) activity with HRV from PPI without awareness of the issue on another variability except CANS activity. Fifteen young male subjects were participated in this study. Simultaneous PPG and ECG were recorded with a portable device in three different postures; supine, sitting and upright positions. Our results show that, although there are no significant differences on heart rate between R-R interval (RRI) and pulse peak interval (PPI), analytic outputs on HRV analyses between RRI and PPI are different; especially, in upright position, there are significant differences on LF and HF (p<; 0.05) and also Tone-Entropy plots are clearly distant between RRI and PPI. In conclusion, our results indicate that PPG should not be used for measurement of CANS activity from HRV because of analytic error depending on physiological states like posture change though PPG probably has little problem to be used as a heart rate monitor.