Magnetic resonance imaging has proven to be useful in the assessment of patients with complex congenital heart disease and in the post-surgical follow-up of patients with corrected congenital heart disease. A thorough understanding of the congenital cardiac malformations that can be encountered is needed and the use of the sequential segmental analysis helps to standardize the evaluation and diagnosis of (complex) congenital heart disease. After surgical correction of congenital heart defects, patients must be followed over extended periods of time, because morphological and functional abnormalities may still be present or may develop. The use of echocardiography may be hampered in these patients as scar tissue and thorax deformities limit the acoustic window. Magnetic resonance imaging has proven to be advantageous in the follow-up of these post-surgical patients and with the use of several different techniques the morphological as well as functional abnormalities can be evaluated and followed over time.