Congenital cardiac malformations which include isomerism of the atrial appendages are amongst the most challenging of problems for diagnosis and also for medical and surgical management. The nomenclature for pathological description is controversial, but difficulties can be overcome by the use of a segmental approach. Such an approach sets out the morphology and the topology of the chambers of the heart, together with the types and modes of the atrioventricular, ventriculo-arterial, and venous connections. We have applied this method to a study of 35 hearts known to have isomerism of the atrial appendages. We have already published accounts of 27 of these cases, but these were reviewed for this study in the light of our increased awareness of the implications of isomerism, and 8 new cases were added. After examining, or re-examining, the morphology of every heart in detail, we grouped them together according to their ventricular topology and modes of atrioventricular connection. Then we studied the course of the specialised conduction system, by the use of the light microscope, first in each individual case, and then together in their groups. We conclude that the pathways for atrioventricular conduction in hearts with isomerism of the atrial appendages are conditioned both by ventricular topology, and by the atrioventricular connections. Based on our experience, we have been able to establish guidelines that direct the clinician to the likely location of the conduction tissues.