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In this study, we examined the structure of the heart of the whale shark, Rhincodon typus, using a plastination technique and three-dimensional X-ray computer tomography (3DCT). Inspection of the atrium revealed a symmetric distribution of the pectinate muscles attached to the commissures of the sino-atrial valve, suggesting some functional advantages. The majority of the ventricular wall comprised spongiosa, and compacta accounted for only ~3% of the entire thickness. There were three major fiber orientations in the spongiosa: the fibers on the endocardial side formed trabeculae that were aligned with the blood flow tract, whereas those on the epicardial side formed a circular pattern around the flow tract. Transmural myofibers connected the inner and outer layers in the spongiosa, which may serve as an intraventricular conduction pathway. Plastination and 3DCT is a powerful combination that allowed for multifaceted visualization of the internal structure of rare heart specimens in a nondestructive manner. Anat Rec, 301:1801-1808, 2018. © 2018 Wiley Periodicals, Inc.