The septal atrioventricular junction is a centrally located region of the heart where the septal components of the atria and ventricles meet the aortic, mitral, and tricuspid valves. Important structures in this region include the membranous septum, the central fibrous body, the Koch triangle, the inferior pyramidal space, and the base of the interventricular septum. This small area is the home of the atrioventricular node and the atrioventricular conduction axis and has enormous importance to electrophysiologists owing to its prime role in the conduction system of the heart. The atrioventricular node lies within the triangle of Koch; and the atrioventricular bundle, or bundle of His, exits the atrioventricular node and penetrates the right fibrous trigone and runs underneath the membranous septum. The septal atrioventricular junction is a common location for intracardiac shunts such as membranous and perimembranous septal defects. Imaging classification of these defects can have important implications before surgical closure, because the atrioventricular conduction axis passes along the posteroinferior margin of most perimembranous defects. Extracardiac inflammatory and malignant pathologic conditions can extend from the mediastinum toward the inferior pyramidal space in this region through the epicardial fat planes. Although the anatomic structures are complicated, the components can be shown in exquisite detail with computed tomography (CT). In this review, the anatomic boundaries and important anatomic landmarks are examined with CT and magnetic resonance imaging. Also described are the anatomic variants of the membranous septum pertinent to percutaneous aortic valve implantation, the vascular anatomic variants, and commonly encountered pathologic conditions related to the septal atrioventricular junction. RSNA, 2016.