The substantia nigra and subthalamic nucleus are two key structures in the midbrain that are very important in movement disorders, particularly those associated with parkinsonism. Using conventional magnetic resonance (MR) imaging, the anatomic description of both these structures can be challenging. This article describes the importance of understanding the underlying anatomy and some of the changes associated with pathology in these structures. Advances in MR imaging are discussed, including high-field MR imaging, diffusion tensor imaging, inversion-recovery imaging, and susceptibility-weighted imaging, with particular reference to the substantia nigra and subthalamic nucleus. Understanding of MR imaging features of these nuclei needs to be firmly based on underlying knowledge of anatomy and pathology from postmortem studies, and more work is needed in this field.