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Summary Background The classic management of neonates with pulmonary atresia with ventricular septal defect (PAVSD) and moderately hypoplastic pulmonary arteries is usually a systemic to pulmonary artery shunt or ductus arteriosus stenting. We report our experience of transcatheter treatment of PAVSD by perforation followed by balloon dilation of the valve, as it is performed in pulmonary atresia – intact ventricular septum. Patients and method Three patients were treated at a mean age and weight of 7.5 days (range 7–8) and 2.9 kg (range 2.5–3.3), respectively. Two newborns were prenatally diagnosed, with micro deletion 22q11 in one case. The three patients had no other pulmonary blood flow support than the ductus arteriosus and were on prostaglandin E1 infusion. The pulmonary atresia was predominantly valvular without significant muscular obstruction. By echocardiography, the mean size of the pulmonary annulus was 6.5 mm (range 6–7). In all cases, the valvular perforation was performed with a 0.014 coronary guidewire, followed by balloon dilation when successfully. Results The procedure succeeded in two cases but failed in the third newborn in whom a long subvalvar muscular stenosis was found at surgery. In the two successful cases, the mean postprocedural transpulmonary doppler gradient was 33.5 mmHg (range 17–50). One patient experienced a femoral venous thrombosis that was successfully treated by heparin and a transient right bundle branch block occurred in another one. In the two successful cases, the prostaglandin E1 infusion was weaned and the surgical repair was performed at 4 and 12 months, respectively. Conclusion In selected cases with PAVSD, perforation followed by balloon dilation of the pulmonary valve offers an interesting alternative to other surgical or transcatheter palliative therapies.