The brainstem has an ectodermal origin and is composed of 4 parts: the diencephalon, mesencephalon, pons, and medulla oblongata. It serves as the connection between the cerebral hemispheres with the medulla and the cerebellum and is responsible for basic vital functions, such as breathing, heartbeat blood pressure, control of consciousness, and sleep. The brainstem contains both white and gray matter. The gray matter of the brainstem (neuronal cell bodies) is found in clumps and clusters throughout the brainstem to form the cranial nerve nuclei, the reticular formation, and pontine nuclei. The white matter consists of fiber tracts (axons of neuronal cells) passing down from the cerebral cortex--important for voluntary motor function--and up from peripheral nerves and the spinal cord--where somatosensory pathways travel--to the highest parts of the brain. The internal structure of brainstem, although complex, presents a systematical arrangement and is organized in 3 laminae (tectum, tegmentum, and basis), which extend its entire length. The motor pathway runs down through the basis, which is located at the most anterior part. The cranial nerve nuclei are settled into the middle layer (the tegmentum), just in front of the 4th ventricle and are placed, from medial to lateral, on the basis of their function: somatic motor, visceral motor, visceral sensory, and somatic sensory. All the somatosensory tracts run upward to the thalamus crossing the tegmentum in front of the cranial nerve nuclei. The tectum, formed by the quadrigeminal plate and the medullary velum, contains no cranial nuclei, no tracts and no reticular formation. The knowledge of precise anatomical localization of a lesion affecting the brainstem is crucial in neurological diagnosis and, on this basis, is essential to be familiar with the location of the mayor tracts and nuclei appropriately. Nowadays, current magnetic resonance imaging techniques, although still macroscopic, allow the fine internal structure of the brainstem to be viewed directly and make it possible to locate the main intrinsic structures that justify the symptoms of the patient. In this article we discuss the anatomy of the brainstem and highlight the features and landmarks that are important in interpreting magnetic resonance imaging.