An indexed offset distance of the tricuspid septal leaflet ⩾8 mm/m2 is a quantitative criterion for the diagnosis of Ebstein's anomaly. The purpose of this study was to investigate the validity of this criterion for the discrimination of Ebstein's anomaly from pulmonary atresia with intact ventricular septum in neonatal patients. A total of 122 neonatal patients, 56 with Ebstein's anomaly and 66 with pulmonary atresia with intact ventricular septum, were enrolled. Diagnosis of each anomaly was based on typical morphologic features. Echocardiographic variables, including the offset distance of the tricuspid septal leaflet, were measured via an offline analysis of images recorded before 1 month of age. The offset distance of the tricuspid septal leaflet was indexed by the body surface area, and the indexed offset distances in the Ebstein's anomaly and pulmonary atresia with intact ventricular septum groups were 34.2 mm/m2 (7.1-119.1 mm/m2) and 7.2 mm/m2 (0.0-25.6 mm/m2), respectively. The indexed offset distance was ⩾8 mm/m2 in 29 (43.9%) of the patients with pulmonary atresia with intact ventricular septum; clinical and echocardiographic characteristics were comparable between these 29 patients and the remaining 37 patients with pulmonary atresia with intact ventricular septum. When an indexed offset distance ⩾8 mm/m2 was applied as a cut-off for the diagnosis of Ebstein's anomaly, the sensitivity was 0.963 and the specificity was 0.561. In conclusion, indexed offset distance ⩾8 mm/m2 cannot be used as a cut-off for the diagnosis of complicated Ebstein's anomaly in neonatal patients with pulmonary atresia with intact ventricular septum.