Both heart rate variability (HRV) and pulse rate variability (PRV) are noninvasive means for the assessment of autonomic nervous control of the heart. However, it is not settled whether or not the PRV obtained from either hand can be the surrogate of HRV. The HRV measures obtained from electrocardiographic signals and the PRV measures obtained from the pulse waves recorded from the index fingers of both hands were compared in normal subjects by using linear regression analysis and Bland and Altman method. Highly significant correlations (P < 0.001, 0.89 < r < 1.0) were found between all HRV measures and the corresponding PRV measures of both hands. However, there were insufficient agreements in some measures between pairwise comparisons among HRV, right PRV and left PRV except heart rate and ultra-low frequency power (ULFP). The PRV of either hand is close to, but not the same as the HRV in healthy subjects. The HRV, right PRV and left PRV are not surrogates of one another in normal subjects except heart rate and ULFP. Since HRV is generally accepted as the standard method for the assessment of the autonomic nervous modulation of a subject, the PRV of either hand may not be suitable for the assessment of the cardiac autonomic nervous modulation of the subject.