Our goal in this study was to compare cardiac autonomic control at rest between 50 individuals with Down syndrome and 24 control participants without disabilities. Resting autonomic function was assessed using analysis of heart rate variability. Participants with Down syndrome had reduced total heart rate variability, which indicates possible autonomic dysfunction in this population. Their VO2peak and BMI were not significantly correlated with resting cardiac autonomic control. This may suggest that fitness level and obesity differentially affect cardiac autonomic control in persons with Down syndrome compared to their healthy, nondisabled peers.