BACKGROUND: Recently, attempts have been made to use the pulse rate variability (PRV) as a surrogate for heart rate variability (HRV). PRV, however, may be caused by the fluctuations of left ventricular pre-ejection period and pulse transit time besides HRV. We examined whether PRV differs not only from HRV but also depending on the measurement site. RESULTS: In five healthy subjects, pulse waves were measured simultaneously on both wrists and both forearms together with single-lead electrocardiogram (ECG) in the supine and sitting positions. Although average pulse interval showed no significant difference from average R-R interval in either positions, PRV showed greater power for the low-frequency (LF) and high-frequency (HF) components and lower LF/HF than HRV. The deviations of PRV from HRV in the supine and sitting positions were 13.2% and 7.9% for LF power, 24.5% and 18.3% for HF power, and - 15.0% and - 30.2% for LF/HF, respectively. While the average pulse interval showed 0.8% and 0.5% inter-site variations among the four sites in the supine and sitting positions, respectively, the inter-site variations in PRV were 4.0% and 3.6% for LF power, 3.8% and 4.7% for HF power, and 18.0% and 17.5% for LF/HF, respectively. CONCLUSIONS: These suggest that PRV shows not only systemic differences from HRV but also considerable inter-site variations.