Echocardiography and cardiac magnetic resonance imaging are the most commonly performed diagnostic studies in patients with congenital heart disease. A small percentage of patients with congenital heart disease will be referred to cardiac CT subsequent to echocardiography when magnetic resonance imaging is insufficient, contraindicated, or considered high risk. The most common complex lesions referred for CT at our institution are tetralogy of Fallot, transposition complexes, and single ventricle heart disease. This review discusses the most common surgical procedures performed in these patients and the technical considerations for optimal image acquisition on the basis of the prior procedure and the individual patient history. Cardiac CT can provide the functional and anatomic information required for decision making in complex congenital heart disease. Image interpretation is aided by knowledge of the common approaches to operative repair and the residual hemodynamic abnormalities. Acquisition and interpretation that is both individualized to the patient's underlying disease and the specific clinical question is likely to maintain diagnostic accuracy while decreasing the potential risk of cardiac CT.