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Segmental pulmonary hypertension is a complex condition in children that encompasses many congenital heart diseases including pulmonary atresia with ventricular septal defect, hemitruncus/truncus arteriosus with branch pulmonary artery stenosis, unilateral absent pulmonary artery, and several post-tricuspid shunt lesions. Multimodality imaging is required to confirm and assess pulmonary vascular disease in subjects with major aorto-pulmonary collaterals. We describe 3 children with complex congenital heart defects who have a variable degree of segmental pulmonary hypertension and discuss management strategies and the role of interventional and/or pulmonary hypertension targeted therapies.