Traditional assessments of autonomic nervous system function have depended on invasive and complex procedures. Vagal power, which is the respiratory component of heart rate variability (HRV) is an alternative and non-invasive measure for indexing autonomic nervous control of the heart. In the current study, 18 multiple sclerosis (MS) and 20 healthy subjects matched with respect to age, education and intelligence served as subjects. The MS group showed significantly lower vagal power during natural and paced breathing than healthy subjects. Importantly, heart rate did not differ between the two groups. If MS patients exhibit abnormalities in mechanisms mediating cardiac parasympathetic control, the impact on quality of life and vulnerability to adverse cardiac events need to be further evaluated. The results of this study may have implications with respect to the feasibility of using HRV as both a diagnostic and prognostic tool for evaluating parasympathetic nervous system dysfunction and in providing valuable information for developing more effective treatment and rehabilitation strategies.