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Prospective electrocardiography (ECG)-gated cardiac computed tomography angiography (CTA) is widely used for pediatric patients with congenital heart disease (CHD) due to the lower radiation dose compared with the ECG-gated technique. However, functional parameters acquired using ECG-gated cardiac CT to predict pulmonary hypertension (PH) in children with CHD have not yet been reported. This study aimed to investigate the potential of diastolic and systolic right ventricular diameters (RVD) on prospective ECG-gated cardiac CTA to predict PH in children with CHD. A total of 44 children with CHD were divided into two groups: CHD with PH (n = 22) and CHD without PH (n = 22). The association between ECG-gated CTA parameters and PH was evaluated by logistic regression. The receiver operating characteristic curve (ROC) was used to find the best cut-off point for the parameters measured by Youden's index. Patients with higher RVD-BSA [aOR (95% CI) diastolic: 2.76 (1.23–6.23); systolic: 6.15 (1.72–22.06)] had higher risk of PH after adjusting for age and patent ductus arteriosus. The area under the curve (AUC) of D-RVD-BSA was 0.907 and the AUC of S-RVD-BSA was 0.917. Logistic regression showed that patients with D-RVD-BSA over 6.86 or S-RVD-BSA over 5.87 had significantly higher risk of PH after adjustments (aOR = 23.52, 95% CI = 2.89–191.03; aOR = 31.14, 95% CI = 2.75–352.85). In conclusion, in children with CHD, measurements of diastolic or systolic BSA-modified RVDs on prospective ECG-gated CTA are non-invasive markers of PH. BSA-modified D-RVD of 6.86 or BSA-modified S-RVD of 5.87 may be used to identify PH in children with CHD. • In children with PH, an association is found between ECG-CTA-gated image parameters and PH. • Diastolic-RVD & systolic-RVD are associated with pulmonary arterial systolic pressure. • Patients with D-RVD-BSA over 6.86 had significantly higher risk of PH. • Patients with S-RVD-BSA over 5.87 had significantly higher risk of PH. • The AUCs of diastolic-RVD and systolic-RVD were 0.907 and 0.917, respectively. [ABSTRACT FROM AUTHOR]