Atrial isomerism and visceral heterotaxy describe complex pathoanatomic findings with defects in the determination of lateralization. Differentiation of right and left atrial isomerism was based on the anatomy of the atrial appendages and bronchial tree and often associated with asplenia in right atrial isomerism and polysplenia in left atrial isomerism. In these pa tients complex cardiac anomalies determine clinical symptoms and diagnostic procedures. At primary diagnosis in the neonatal period, systemic venous and pulmonary venous connections and intracardiac anatomy are identified using the sequential segmental approach. Therapeutic decisions and palliative procedures can usually be based on these initial echocardiographic findings. As many of the patients were found to have a functionally univentricular heart, surgical procedures following the Fontan principle (lateral tunnel or extracardiac conduit procedure) were introduced in patients with heterotaxy syndrome and successfully performed. Early survival and long-term outcome vary depending on associated cardiac and systemic and pulmonary venous anomalies. The therapeutic options and mid-term results in patients with heterotaxy syndrome undergoing the Fontan procedure are reported.