The objective of this study was to analyze the echocardiographic characteristics of juxtaposition of the atrial appendages and to determine its prevalence in children with congenital heart disease. From June 1998 to December 2008, 10,880 children underwent selective angiocardiography, magnetic resonance imaging (MRI), and echocardiography for evaluation of congenital heart disease. Juxtaposition of the atrial appendages was diagnosed based on the results of angiocardiography and MRI; the echocardiographic characteristics of this anomaly were analyzed retrospectively. There were 33 patients diagnosed with juxtaposition of the right atrial appendage (JRAA); no patient was diagnosed with juxtaposition of the left atrial appendage. The prevalence of JRAA in children with congenital heart disease was 0.30%. JRAA and abnormal spatial orientation of the atrial septum were visualized by Doppler echocardiography in 28 cases. In the remaining five cases, three cases with suspected JRAA could not be determined by echocardiography and the diagnosis was missed in two cases. The most common associated anomalies were conotruncal malformations (16 cases with double outlet of the right ventricle, 9 cases with pulmonary atresia, 6 cases with transposition of the great arteries, 1 case with tetralogy of Fallot) and tricuspid malformations (6 cases with tricuspid straddling, 3 cases with tricuspid atresia, 2 cases with tricuspid valve stenosis). Based on the characteristic alteration of the plane of the atrial septum and visualization of the malpositioned right atrial appendage, JRAA can be accurately diagnosed by Doppler echocardiography.