Objectives. The aim of this study was to assess the morphology of the coronary sinus, its drainage and associated cardiac malformations when there is either complete unroofing of the coronary sinus or atresia of its connection to the right atrium. Background. As more children with complex cardiac anomalies are accepted for primary surgical repair or palliation with cavopulmonary anastomoses, a knowledge of coronary sinus and systemic venous anomalies is important if coronary venous return is to be preserved and residual shunts avoided. Methods. Twenty-six heart-lung specimens without a coronary sinus draining to the right atrium were identified from the Leiden collection of congenital heart malformations. These were classified into specimens with an unroofed coronary sinus and those with atresia of the coronary sinus orifice. Attention was paid to the associated cardiac malformations. Results. In 14 (54%; confidence limits [CL] 35%, 73%) of 26 specimens, there was an unroofed coronary sinus, associated with persistence of the left superior caval vein. An inferoposterior location of an atrial septal defect was detected in 2 (14%; CL –4%, 33%) of 14. Atrial appendage anomalies were seen in 13 (93%; CL 79%, 106%) of 14 specimens, exemplified by both right and left isomerism. These were frequently associated with an atrioventricular septal defect (12 [86%; CL 67%, 104%] of 14). An atretic coronary sinus orifice was seen in 12 (46%; CL 27%, 65%) of 26. Atrial appendage anomalies (2 [17%; CL –4%, 38%] of 12) were rare in these cases. The drainage was then by way of a left superior caval vein or, in its absence, a coronary sinus to left atrial window. Ventricular hypoplasia was seen in both categories of coronary sinus abnormalities. Important ventricular hypoplasia was seen in 12 cases (46%; CL 27%, 65%). Conclusions. These findings emphasize the need to study coronary sinus drainage before procedures such as ligation or transcatheter coil embolization of a left superior caval vein, venous redirection or closure of a dorsal atrial septal defect are contemplated. These procedures might inadvertently lead to impairment of coronary venous return or persistence of an intracardiac shunt.