We reviewed our 28 years of experience of arterial switch operation (ASO) for transposition of the great arteries to investigate late sequelae of this procedure. 387 patients who underwent ASO from 1984 to 2010 were included in this retrospective study. The longitudinal data were estimated by the Kaplan-Meier method and compared using a log-rank test. Risk factors for late sequelae were analysed by the multivariable Cox proportional hazards model. The mean follow-up time was 10.0 years. There were 13 early deaths and 17 late deaths. All late deaths were within 1 year, except for three patients. Actuarial survival was 92.2 and 91.6% at 10 and 20 years, respectively. Sixty-six patients (17.1%) had developed pulmonary stenosis (PS) and 29 patients (7.5%) had developed moderate or more aortic insufficiency (AI) during follow-up. Selective coronary angiography was performed in 210 patients (54.3%) at 9.6 +/- 5.1 years after ASO. Left main tract occlusion was found in 2 patients (2/210; 1.0%) and hypoplastic left coronary artery was found in 10 patients (10/210; 4.8%). Among these 12 patients, 8 patients were asymptomatic. Re-operation was performed in 76 patients (19.6%), pulmonary artery plasty for PS in 58 patients (15.0%), aortic valve replacement for AI including two Bentall operations in 9 patients (2.3%) and others. Freedom from re-operation was 78.2 and 62.8% at 10 and 20 years, respectively. The risk factor for PS was the use of equine pericardium for reconstruction (P < 0.0001). Factors associated with moderate or more AI was the presence of left ventricular outflow tract obstruction (P = 0.004). There were no risk factors for late coronary lesions. Three hundred and forty surviving patients (340/357; 95.2%) were in NYHA functional class I. Treadmill test, which was performed on 217 patients (56.1%) at 14.3 +/- 5.4 years after ASO, revealed that the maximum heart rate was 97.5 +/- 7.6% of normal and peak oxygen consumption was 105.2 +/- 20.5% of normal. ASO was performed with satisfactory results in the overall survival and functional status. PS was the main reason for re-operation. Coronary lesions can appear late without any symptoms. Benefits of ASO can be achieved by long-term follow-ups of PS, AI and coronary lesions.