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We investigated how complexity-based estimators of heart rate variability can detect changes in cardiovascular autonomic drive with respect to traditional measures of variability. This was done by analyzing healthy subjects and paraplegic patients with different autonomic impairment due to low (vascular impairment only) or high (cardiac and vascular impairment) spinal cord injury, during progressive autonomic activations. While traditional techniques only quantified the effects of the autonomic activation, not distinguishing the effects of the lesion level, some recently proposed complexity estimators could also reveal the pathologic alterations in the autonomic control of heart rate. These estimators included the detrended fluctuation analysis coefficient (sensitive to both low and high autonomic lesions), sample entropy (sensitive to low-level lesions) and the largest Lyapunov exponent (sensitive to high-level lesions). Thus complexity-based methods provide information on the autonomic function from the heart rate dynamics that cannot be obtained by traditional techniques. This finding supports the combined use of both complexity-based and traditional methods to investigate the autonomic cardiovascular control from a more comprehensive perspective.