Magnetic resonance imaging is a powerful diagnostic tool, able to give us accurate anatomical and functional insights concerning the structure of the heart, and capable of overcoming some of the drawbacks and limitations of echocardiography and catheterization. The aim of our current review is to highlight the advantages and applications of the technique in the evaluation of patients with functionally univentricular hearts before and after conversion to the Fontan circulation. Most of these patients will have undergone surgery several times in their life, with a certain body size, and with less than optimal echocardiographic windows because of the surgical scars. Moreover, vascular access is sometimes unavailable due to previous catheterizations. Furthermore, resonance imaging is non-invasive, and can be performed without sedation in patients older than 8 years. Since many of the current techniques, some of them still experimental, will be used extensively in future clinical practice, physicians should be aware of the full spectrum of capabilities of resonance imaging. We will highlight all these applications in the sections which follow.