Magnetic resonance imaging (MRI) techniques have emerged as powerful tools for unraveling the pathophysiology of rare diseases, mainly due to their pivotal role in early diagnosis, disease characterization, and treatment monitoring in a non-invasive manner. In this chapter, we will review two essential MRI tools used for studying and evaluating the pathophysiology of Allan-Herndon-Dudley Syndrome or MCT8 deficiency, a rare disease caused by inactivating mutations in the SLC16A2 gene, encoding for the thyroid hormone-specific transmembrane transporter MCT8. These two MRI techniques are time-of-flight magnetic resonance angiography (TOF-MRA) and diffusion tensor imaging (DTI).