We describe an intracardiac epithelial cyst in association with esophageal atresia. The case is unusual in that the cyst was symptomatic and ultimately fatal. In addition, there was no other cardiac anomaly, although a range of extrathoracic malformations was present. There are three types of intracardiac epithelial cysts: congenital polycystic tumor of the atrioventricular node, a cyst as part of a teratoma, and, as in this case, a gross cyst. All of them are very rare. The association of a cardiac cyst and esophageal atresia in our case supports the theory that intracardiac cysts are derived from misplaced foregut.