Introduction: The first step in diagnosing congenital cardiac malformations is to assess the arrangement of the atrial appendages. In patients with abnormal lateralization of the organs of the body, the arrangement of atrial appendages is neither normal, nor a mirror image of normal. There are 2 categories of abnormal arrangement based on the morphology of the atrial appendices, namely right isomerism and left isomerism, and in almost all instances these are found in the setting of so-called heterotaxy syndromes. Objective: To evaluate the various congenital cardiac malformations those are associated with abnormalities of lateralization, and to discuss the diagnostic tools, therapeutic options, and outcome for these patients. Patients and methods: We studied 134 patients, who had been admitted to our department of paediatric cardiology with known abnormalities of lateralization and congenital cardiac defects between 1990 and 2003. The data relating to each patient was evaluated retrospectively. The arrangement of the atrial appendages was established echocardiographically, and/or angiographically, and/or on the basis of morphologic investigations during the operation. These studies showed that 43 (32.1%) of the patients had right isomerism, and 88 (65.7%) had left isomerism. In 2 (1.5%), there was mirror-imaged arrangement, while in the final patient (0.07%), we were unable to determine sidedness with certainty. The median age at diagnosis was 0.66 years, and the females outnumbered the males in a ratio of 3 to 1. Patients in the 2 isomeric groups were compared with regard to age, cardiac defects, diagnostic tools and outcomes. Results: The difference in mean ages of the two groups of patients was statistically significant, those with right isomerism being 1.0 minus or plus 1.5 years, as opposed to those with left isomerism being 3.3 minus or plus 4.7 years (P is less than 0.005). Of the patients with right isomerism, 32 (74.4%) had left-sided, and 11 (25.6%) right-sided hearts, whereas in those with left isomerism, the hearts were left-sided in 65 (73.9%), and right-sided in 21 (23.9%), with 2 (2.2%) positioned in the midline. Extracardiac totally anomalous pulmonary venous connection was more common in those with right isomerism, being found in 13 patients (30.2%) as opposed to 5 patients (5.7%) with left isomerism. In only 8 of those with right isomerism did we find two perforate atrioventricular valves (18.6%), this arrangement being found in 34 (38.6%) of those with left isomerism. Pulmonary atresia and stenosis were present in 40 (93.0%) of those with right isomerism, but also in 41 (46.6%) of the patients with left isomerism. Angiographic and echocardiographic investigations were concordant in about three-quarters of patients with both right and left isomerism. All patients with extracardiac totally anomalous pulmonary venous connection died. Overall, 22 of the patients with right isomerism died (51.2%), as opposed to 20 (22.7%) of those with left isomerism. Conclusion: Our experience confirms that patients with right isomerism have more complex cardiac defects than those with left isomerism. Overall, the presence of isomerism carries a poor prognosis, the more so for right isomerism, with this related to the complex cardiac abnormalities. In our cohort, extracardiac totally anomalous pulmonary venous connection with pulmonary arterial obstruction was always a fatal combination. The mapping of cardiac and abdominal morphologies is still essential for proper diagnosis of these syndromes, especially in fetal life.