A review examined six consecutive cases of patients with esophageal atresia (EA) and tracheoesophageal fistula (TEF) who underwent cardiac surgery at the authors’ institution between 2001 and 2011 for associated complex congenital heart diseases. All the patients had a normal karyotype and showed EA with distal TEF. In all cases, gastrostomy was the initial surgical intervention. Cardiac surgery was performed concurrently with gastrostomy for one patient who had a total anomalous pulmonary venous connection with pulmonary venous obstruction. For two patients with duct-dependent pulmonary circulation, EA/TEF was corrected in the neonatal period, and an aortopulmonary shunt operation was electively performed after the first month of life. For two patients with duct-dependent systemic circulation, repair of EA/TEF was performed concurrently with gastrostomy, followed by palliative cardiac surgery during the neonatal period. For another patient without duct-dependent circulation, repair of EA/TEF was performed in the neonatal period. No mortality occurred during a median follow-up period of 6.2 years. However, respiratory complications including severe tracheomalacia for two patients, recurrent episodes of respiratory infection for three patients, and severe gastroesophageal reflux for five patients caused considerable long-term morbidity.