BACKGROUND: Because the conventional evaluation of autonomic nervous system (ANS) function inevitably uses long-lasting uncomfortable electrocardiogram (ECG) recording, a more simplified and comfortable analysis system has been sought for this purpose. The feasibility of using a portable micro-electromechanical system (MEMS) blood flowmeter to analyze heart rate variability (HRV) for evaluating ANS function was thus examined. METHODS AND RESULTS: Measurements of the R-R interval (TRR) derived from an ECG, simultaneously with the pulse wave interval (TPP) derived from a MEMS blood flowmeter, in 8 healthy subjects was performed and resultant HRV variables in time and frequency domains were compared. The TRR- and TPP-derived variables were strongly correlated (coefficients of regression for low frequency (LF), high frequency (HF), and LF/HF of 1.1, 0.66, and 0.35, respectively; corresponding coefficients of determination of 0.92, 0.63, and 0.91, respectively (P<0.01)). In addition, the values of LF, HF, and LF/HF, as analyzed using TPP, changed significantly from the supine to the standing position in another 6 subjects. CONCLUSIONS: Miniaturized-MEMS blood flowmetry can be used to perform HRV analysis for the evaluation of ANS function, which is as accurate as analysis based on ECG within comparable tolerances. As MEMS blood flowmetry can more easily and comfortably record physiological variables for longer durations than ECG recording, and can further capture skin blood flow information, this device has great potential to be used in a wider area of physiological analyses.