Those using the mouse for the purposes of electrophysiological research presume that the morphology of the conduction axis is comparable with the human arrangement. As yet, however, to the best of our knowledge, no direct comparison has been made between the species. By comparing our extensive histological findings in the human heart with comparable serially-sectioned datasets prepared from adult murine hearts, we aimed to provide this information. When comparing the gross anatomy, we used three-dimensional datasets of neonatal mice hearts prepared using episcopic microscopy. The overall cardiac architecture is comparable, although the mouse has a persistent left superior caval vein draining via the coronary sinus. An inferior pyramidal space and an infero-septal recess are both present in the murine heart, although they are not as well developed as in the human heart. The overall arrangement of the conduction axis is similarly comparable, albeit with subtle differences reflecting the incomplete wedging of the subaortic outflow tract in the murine heart. Most significantly, the findings in both species reveal the presence of extensive superior septal pathways, which perhaps explain the finding of base-to-apex activation of the ventricular mass known to occur in the murine heart.