Objectives To describe our experience with percutaneous closure of patent ductus arteriosus (PDA) in small infants and compare outcomes to matched surgical patients. Background Ligation via thoracotomy has been used to close PDAs in small infants, but has been associated with respiratory and hemodynamic compromise. We hypothesized that percutaneous closure would offer faster recovery of respiratory function. Methods Patients <4 kg requiring positive pressure ventilation who underwent percutaneous PDA closure between January 2000 and April 2012 were reviewed and matched to contemporary surgical patients on gestational age (GA), birth weight (BW), procedure weight (WT), and ventilation mode. Patients returned to baseline respiratory status when the product of mean airway pressure and FiO2 returned to pre-procedural levels. Results Eight matched pairs were included. Median BW, GA, and WT were 1.43 kg (0.52-2.97), 29.8 weeks (24-39), and 2.8 kg (2.2-3.9) for catheter patients and 1.55 kg (0.48-3.04), 29 weeks (23-37), and 2.75 kg (2.3-4.2) for surgical patients. Complete PDA closure occurred in all. The median time to return to baseline respiratory status was significantly shorter in the percutaneous group (17 hr (range 0-113) vs. 53 hr (range 13-219), P < 0.05). In the percutaneous group, two patients developed mild aortic coarctation, one mild left pulmonary artery stenosis, and four femoral vascular thromboses which all resolved with medical therapy. Surgical complications included significant respiratory and cardiac compromise, rib fractures and urinary retention. Conclusions Percutaneous closure of PDA in small infants on respiratory support is equivalent in safety and efficacy and may offer shorter recovery time than surgical ligation.