We report the first-stage percutaneous palliation in a newborn with a rare heterotaxy syndrome variant including interrupted inferior vena cava, partial anomalous pulmonary venous drainage, and restrictive interatrial communication. Virtual reality imaging aided visualisation, decision-making, and planning. Successful atrial septoplasty performed via the internal jugular vein and anomalous pulmonary vein was followed by stenting of ductus arteriosus.