The ejection fraction of the trabeculated cardiac ventricle of reptiles has not previously been measured. Here we use the gold standard clinical methodology – electrocardiogram (ECG) gated flow magnetic resonance imaging (MRI) – to validate stroke volume measurements and end diastolic ventricular blood volumes. This produces an estimate of ejection fraction in the red footed tortoise Chelonoidis carbonaria (n=5) under isoflurane anaesthesia of 88±11%. After elimination of the prevailing right-to-left intraventricular shunt through the action of atropine, the ejection fraction was 96±6%. This methodology opens new avenues for studying the complex hearts of ectotherms, and validating hypotheses on the function of a more highly trabeculated heart than that of endotherms which possess lower ejection fractions.