The development of the midbrain and hindbrain occurs between the fifth and tenth weeks of gestation as part of ventral induction. As the neural tube closes, three primary cephalic vesicles develop—prosencephalon, mesencephalon, and rhombencephalon (Cotes et al. 2015). The mesencephalon and rhombencephalon are separated rostrally from the prosencephalon by the cephalic flexure and separated caudally from the spinal cord by the cervical flexure. This chapter reviews the brainstem features of aqueductal stenosis, Chiari malformations, and abnormal nuclear and tract arrangements, with particular attention to ciliopathis, tubulinopathies, brainstem cap dysplasias, and dysplasias affecting the inferior olivary nuclear complex.