An infant with ventricular septal defect, atrial septal defect, and Down syndrome (trisomy 21) was referred to our institution. The patient gradually developed infantile lobar emphysema of the right upper lobe and became dependent on mechanical ventilator support. When the patient was five months of age, we successfully performed a total correction of cardiac anomalies combined with a right upper lobectomy. The resection of the right upper lobe was performed under cardiopulmonary bypass through a median sternotomy. There was no major airway bleeding or mediastinitis. The patient was extubated on postoperative day 12 and discharged on postoperative day 29.