Abstract Background Congenital ductus arteriosus aneurysm (DAA) was considered rare but potentially fatal abnormality, often followed by surgical intervention after careful evaluation. This prospective study used real-time three-dimensional echocardiography (RT3DE) to assist in evaluation of neonatal DAA. Methods A total of 1390 full-term neonates were enrolled in this study between 2002 and 2003. They received two-dimensional echocardiographic (2DE) screening and periodic follow-up. RT3DE was performed selectively for newborns with DAA. Results DAA were detected in 116 (8.34%) newborns using 2DE. Maximum diameter of the DAAs ranged from 6.8 to 14.0 mm (8.2 ± 1.1mm). None of the cases were symptomatic or had complications related to DAA. There were no significant differences in sex and gestational age between the newborns with and without DAA. Neonates with DAA had a higher birth body weight and a higher incidence of large-for-gestational-age ( P < 0.05). RT3DE provided instant, consistent and reliable 3D images of DAA and its related structures and allowed for more rapid examination times and reduction of baby wait times. Conclusions Congenital DAA is as common as has been previously reported. RT3DE is useful in assisting evaluation of DAA. Preferred images of DAA were typically visualized in the high parasternal short-axis view before the third day of life. Routine use of RT3DE is suggested to enhance assessment of neonates with DAA detected by 2DE.