Objective To compare the advantages of reconstructing the aorta by end-to-side anastomosis with extended end-to-end anastomosis for aortic coarctation （CoA） with cardiac lesions in neonates and infants. Methods There were 63 neonates and infants who underwent median full sternotomy for correction of CoA and cardiaclesions from January 2008 to July 2011 in Guangzhou Women and Children’s Medical Center. These patients were divided into two groups： extended end-to-end anastomosis was performed in 24 patients （end-to-end group, 17 males and 7 females with their mean age of 4.6±2.9 months）and end-to-side anastomosis in 39 patients （end-to-side group, 24 males and 15 females with their mean age of 3.4±2.6 months）. We compared the two groups with regard to postoperative mortality, morbidity and difference in blood pressure between the lower and upper extremities. Results The percentage of newborn patient（23.1% vs. 4.2%; χ2=3.979, P=0.045）and presence of pre-operative acidosis（15.4% vs. 0%; χ2=4.080, P=0.048）were significantly higher in end-to-side group than those in end-to-end group. There was no postoperative death in end-to-end group and 1 patient died after surgery in end-to-side group（2.6%）. The average duration of circulatory arrest in end-to-side group was significantly shorter than that in end-to-end group （18.6±2.7 min vs.23.4±3.7 min, F=14.617, P=0.000）. At the time back to cardiac intensive care unit, the percentage of patients whose difference in systolic pressure between radial and femoral artery ＜ 5 mm Hg, 5-15 mm Hg, and＞ 15 mm Hg was 20.8%, 45.8% and 33.3% respectively in end-to-end group, and 97.4%, 2.6% and 0% respectively in end-to-side group（χ2=40.380，P=0.000）. Twenty-four hours after surgery, the percentage of patients whose difference in systolic pressure between radial and femoral artery＜ 5 mm Hg, 5-15 mm Hg, and＞ 15 mm Hgwas 45.8%, 41.7% and 12.5% respectively in end-to-end group, and 100%, 0% and 0% respectively in end-to-side group （χ2=26.620, P=0.000）. All the surviving 62 patients were followed up for 2-36 months, and there was no patient with angeioma or re-stenosis needing intervention in either group during follow-up. Conclusion End-to-side anostomosis is a safe and effective method for treating CoA with cardiac lesions and eliminating residual stenosis in neonates and infants.