Balloon angioplasty is an alternative to surgical repair for coarctation of the aorta in children. However, its role in the treatment of neonates and infants younger than 3 months old remains controversial. The purpose of this study was to evaluate the efficacy and safety of balloon angioplasty for native coarctation by comparing children in different age groups. This is a retrospective clinical study including 37 children treated with balloon angioplasty for native coarctation from January 2006 to December 2012. A total of 37 patients consisting of 26 boys and 11 girls underwent the procedure, with median age 10 months (range from 7 days to 6 years) and the mean body weight was 6.3 (2.5-17.0) kg. The indication of the procedure includes discrete native coarctation without aortic arch hypoplasia and a peak-to-peak systolic pressure gradient > 20 mmHg (1 mmHg = 0.133 kPa) across aortic coarctation. During one year follow-up, the approach artery injury, recoarctation and aneurysm formation were particularly assessed. We classified these patients into two groups according to their age. Group A consisted of 25 patients younger than 3 months and Group B of 12 patients older than 3 months. There was no significant difference between the two groups in systolic pressure gradient before balloon angioplasty (P > 0.05). The mean peak systolic gradient decreased from (38 ± 18) mmHg to (12 ± 11) mmHg immediately after angioplasty in group A and from (47 ± 18) to (17 ± 12) mmHg in group B (P = 0.000 for both). Meanwhile, the mean diameter of the coarctation segment increased from (1.8 ± 0.7) to (3.7 ± 1.1) mm after angioplasty in group A and from (2.6 ± 1.5) to (5.5 ± 1.8) mm in group B (both P = 0). The initial successful balloon angioplasty (immediate postangioplasty peak pressure gradient < 20 mmHg) was achieved in all the 37 patients; 32 patients (86.5%) have been followed up for one year. Approach arterial complications occurred in 3 patients (9.4%), all of whom were in Group A (P = 0.537). Two patients had decreased femoral artery pulse and one required surgical repair for a postoperative pseudoaneurysm at left carotid artery. At follow-up, 8 patients (25.0%) developed recoarctation, with 6 cases in Group A and 2 in Group B. There was no significant difference between groups A and B in the recoarctation rate (P = 1.000). Among them, 7 patients underwent repeat balloon angioplasty, and all showed successful relief of coarctation, and one patient required surgical repair. Two patients (2/37, 5.4%) had small aneurysms of the descending aorta immediately after balloon angioplasty, with one patient in each group (12/25 vs.1/12, P = 0.755).Late aneurysm development has not been observed in the 17 patients who have had a follow-up CTA or MRA study. Balloon angioplasty of discrete native coarctation is effective and safe in children both younger and older than 3 months with similar incidence of approach arterial complication, recoarctation and aneurysm formation.