The arterial switch operation (ASO) is widely used nowadays as the surgical strategy of choice to repair transposition of the great arteries (TGA). Residual morphological and geometrical abnormalities of the aorta, pulmonary arteries and coronary arteries, however, have not been fully studied in a three-dimensional (3D) domain. These morphometric complications might have implications on long-term outcomes of ASO patients, hence the need to explore them in detail and study them with reference to healthy controls of comparable age and body surface area. These anatomical characteristics were examined using 3D patient-specific anatomical models reconstructed from cardiovascular magnetic resonance (CMR) images of 20 ASO patients (mean age 14.4 ± 2.4 years, 16 males and 4 females) compared with healthy controls (mean age 15.2 ± 2.0 years, 17 males and 3 females). It was found that the aorta, pulmonary arteries and re-implanted coronary arteries of ASO patients were significantly different morphologically and geometrically to those of healthy controls. In particular, the aortic root was dilated, with abnormal 3D angulation and additional acute angulation of the curvature of the aortic arch in the ASO group compared with controls. This could theoretically impinge on aortic flow profiles and physiological stresses, which can act as a primer for the development of early atherosclerotic disease in the ASO population.