Background: Optimal management strategy for native aortic coarctation in neonates and young infants is a controversial issue. In this study, we compare balloon dilatation with surgery in terms of the efficacy of treating native aortic coarctation in patients less than 120 days of age. Methods: Between January 2000 and October 2006, after excluding patients with complex cardiac anomalies, we enrolled 21 patients with native aortic coarctation in this study. Group 1 included 9 patients who accepted balloon dilatation for discrete isthmic stenosis. Group 2 included 12 patients who underwent surgical aortoplasty by end-to-end anastomosis for long segment stenosis. We compared the demographic data, hospital days, complications, residual gradients and restenosis rates between the two groups. Results: There were no statistical differences between the two groups in terms of the demographic data, age at procedure, immediate pressure relief, restenosis rate or survival rate. Procedure-related complications occurred more frequently after surgical repair compared with angioplasty (p=0.02). Themedian post-procedure hospital stay was shorter in the angioplasty than in the surgery group: 6 days (range, 3 to 82 days) in the angioplasty group and 27 days (range, 7 to 292 days) in the surgery group (p = 0.005). At a median follow-up of 19 months, two group 1 patients had recoarctation requiring surgery, and three group 2 patients also experienced reintervention due to restenosis or severe residual coarctation. Conclusion: These data suggest that balloon angioplasty may be an acceptable alternative to surgical treatment for native discrete aortic coarctation in neonates and young infants.