Perioperative autonomic nervous system (ANS) measurements are evolving toward increasing import and utility. We present a three-year-old male with Down Syndrome who underwent ambulatory autonomic monitoring during surgery followed by cardiac magnetic resonance (CMR) imaging. Autonomic data from both environments are compared to age-related norms. We are the first to describe a method for acquiring and trending autonomic data from clinically indicated CMR scans in order to monitor autonomic function. These data are proof of concept for the use of routinely collected CMR data as a surrogate for autonomic data in children, noting differences in the autonomic effects of anesthetic techniques.