We have analysed the atrioventricular junction, ventricular mass, and ventriculoarterial junction in 43 hearts with isomeric atrial chambers. Of the hearts, 32 had atrial chambers of bilateral right morphology while 11 had atrial chambers with bilateral left atrial characteristics. Among the hearts with right atrial isomerism, there were 13 biventricular hearts, all with ambiguous atrioventricular connection. Eight had a common valve and five had two atrioventricular valves. In the other 19 hearts, the atrial chambers were connected to only one ventricular chamber, 18 having double inlet ventricle through a common valve and the other having absence of the left atrioventricular connection. In these univentricular hearts, all possible types of ventricular morphology were found. The ventriculoarterial junction among these hearts with right isomerism showed great variation. In the hearts with left atrial isomerism, nine hearts had two ventricles and two were univentricular. The biventricular hearts all had ambiguous atrioventricular connection, six via a common valve and three via two valves. The two univentricular hearts both had double inlet via a common valve, one to a chamber of right ventricular type and the other to a chamber of left ventricular type. Both had rudimentary chambers of complementary pattern. The ventriculoarterial junction again showed much variation. Statistical analysis showed that pulmonary obstruction and a univentricular heart were both significantly more frequent in association with right compared with left isomerism. Significant differences were also noted in the two groups in terms of ventriculoarterial connections and infundibular morphology.