A ventricular septal defect in transposition of the great arteries is frequently closely related to the cardiac valves. The valvar function after arterial switch operation of patients with transposition of the great arteries and ventricular septal defect or intact ventricular septum was compared. We analysed the function of all cardiac valves in patients who underwent the arterial switch operations pre- and post-operatively, 1 year after the procedure and on follow-up. The study included 92 patients - 64 with transposition of the great arteries/intact ventricular septum and 28 with transposition of the great arteries/ventricular septal defect. The median age at surgery was 5.5 days in transposition of the great arteries/intact ventricular septum (0-73 days) and 7.0 days in transposition of the great arteries/ventricular septal defect (4-41 days). Follow-up was 51.7 months in transposition of the great arteries/intact ventricular septum (3.3-177.3 months) and 55 months in transposition of the great arteries/ventricular septal defect (14.6-164.7 months). Neo-aortic, neo-pulmonary, and mitral valvar function did not differ. Tricuspid regurgitation was more frequent 1 year post-operatively in transposition of the great arteries/ventricular septal defect (n = 4) than in transposition of the great arteries/intact ventricular septum. The prevalence of neo-aortic regurgitation and pulmonary stenosis increased over time, especially in patients with transposition of the great arteries/intact ventricular septum. The presence of a ventricular septal defect in patients undergoing arterial switch operation for transposition of the great arteries only has a minor bearing for the development of valvar dysfunction on the longer follow-up.