The objective of this study was to evaluate the prevalence of atrial septal aneurysm (ASA) in newborns, to define the natural course of ASA, and to investigate its role on closure of associated interatrial septal opening (IASO). A total of 1072 consecutive neonates were examined with echocardiography in the early postnatal period. The length of the interatrial septum, the diameter of IASO, the excursion and base of aneurysm, and the width of the related atrium were measured and the excursion ratio and the basal ratio were calculated for each neonate. Aneurysms with an excursion ratio > or = 25% were diagnosed as ASA. There were 81 neonates (7.6%) with ASA. The prevalence of ASA was 11.1% in preterm (14 of 126) and 7.1% in full-term newborns (67 of 946). All of the ASAs disappeared at the end of the first year of life, and there were no complications related to the lesion during the follow-up period. Although overall IASO prevalence was 78.6% (843 of 1072), it was 72.8% (59 of 81) among the cases with ASA. Although the disappearance time of interatrial septal shunt was not significantly different between the cases with and without ASA, spontaneous closure was less frequent in the cases with ASA than in those without ASA 77.7 and 96.1%), respectively (p < 0.001). The prevalence of ASA is high among newborns, with a high resolution rate. Therefore, it can be considered that it is benign and transient observation. Less frequent spontaneous closure of IASO in cases with ASA indicates that ASA may have a deleterious effect on spontaneous closure.