The anatomy of the cardiac conduction system in normal and malformed hearts reconstructed from histological serial sections is reviewed. The sinus node and its arterial supply are located in the right superior cavoatrial junction except in hearts with left‐sided juxtaposition of the atrial appendages, mirror‐image, and isomeric arrangements of the atria. In the presence of normally positioned atrial and ventricular septal structures, the triangle of Koch is a useful guide to the location of the atrioventricular node and the penetrating bundle. In hearts with “isolated” ventricular septal defects, it is necessary to distinguish between a perimembranous defect and a muscular inlet defect. The conduction axis runs in the area of fibrous continuity at the posteroinferior edge of a perimembranous defect but in the anterosuperior rim of a muscular inlet defect. In most hearts with tetralogy of Fallot, the danger area is the region of aortic‐mitral‐tricuspid fibrous continuity where the axis penetrates. In hearts with atrioventricular septal defects, the lack of contiguity between atrial and ventricular septum results in a posterior displacement of the nodal triangle and coronary sinus and an elongation of the nonbranching bundle. Hearts with abnormally located atrioventricular nodes and conduction axes are mainly those with atrioventricular discordance, ambiguous atrioventricular connection in presence of left‐hand pattern ventricular topology, hearts with univentricular atrioventricular connection to a morphologically left or indeterminate ventricle, and hearts with a straddling tricuspid valve. The location of the atrioventricular node is governed by the orientation of the ventricular septum and by the pattern of ventricular topology.