Introduction: Photoplethysmography (PPG) has been widely used to assess cardiovascular function. However, few studies have comprehensively investigated the effect of measurement site on PPG waveform characteristics. This study aimed to provide a quantitative comparison on this.Methods: Thirty six healthy subjects participated in this study. For each subject, PPG signals were sequentially recorded for 1 min from six different body sites (finger, wrist under (anatomically volar), wrist upper (dorsal), arm, earlobe, and forehead) under both normal and deep breathing patterns. For each body site under a certain breathing pattern, the mean amplitude was firstly derived from recorded PPG waveform which was then normalized to derive several waveform characteristics including the pulse peak time (Tp), dicrotic notch time (Tn), and the reflection index (RI). The effects of breathing pattern and measurement site on the waveform characteristics were finally investigated by the analysis of variance (ANOVA) with post hoc multiple comparisons.Results: Under both breathing patterns, the PPG measurements from the finger achieved the highest percentage of analyzable waveforms for extracting waveform characteristics. There were significant effects of breathing pattern on Tn and RI (larger Tn and smaller RI with deep breathing on average, both p < 0.03). The effects of measurement site on mean amplitude, Tp, Tn, and RI were significant (all p < 0.001). The key results were that, under both breathing patterns, the mean amplitude from finger PPG was significantly larger and its Tp and RI were significantly smaller than those from the other five sites (all p < 0.001, except p = 0.04 for the Tp of “wrist under”), and Tn was only significantly larger than that from the earlobe (both p < 0.05).Conclusion: This study has quantitatively confirmed the effect of PPG measurement site on PPG waveform characteristics (including mean amplitude, Tp, Tn, and RI), providing scientific evidence for a better understanding of the PPG waveform variations between different body sites.