The interventional cardiac magnetic resonance imaging (iCMR) catheterization procedure is feasible and safe for children and adults with pulmonary hypertension and congenital heart defects (CHD). With iCMR, the calculation of pulmonary vascular resistance (PVR) in children with complex CHD with multilevel shunt lesions is accurate. In this paper, we describe the role of the MRI-guided right-sided cardiac catheterization procedure to accurately estimate PVR in the setting of multiple shunt lesions (ventricular septal defect and patent ductus arteriosus) and to address the clinical question of operability in an adolescent with trisomy 21 and severe pulmonary hypertension.