We repaired secundum atrial septal defect in 135 consecutive patients from February 2003 to December 2010. There were 98 females and 37 males, with a mean age of 22.92 ±17.46 years (range, 3–55 years). To prevent myocardial dysfunction and systemic embolism caused by the conventional technique, the operation was performed with a beating heart under cardiopulmonary bypass in 63 cases, and compared the data retrospectively with cases treated under aortic crossclamping, to determine the safety of the beating-heart technique and to evaluate risk factors for embolism in stroke patients. Patient age and size of defect were similar in both groups. There was no death and no residual shunt in either group. The mean cardiopulmonary bypass time was 36.84 ± 9.8 min in the beating-heart group and 43.13 ± 16.7 min in the crossclamp group. The ejection fraction and the incidence of postoperative arrhythmia were similar in both groups. There were no differences in blood products transfused, intensive care unit stay, hospital stay, or perioperative morbidity. In our experience, the results of the beating-heart technique were not different from the conventional technique.