The brainstem is the most caudally situated and phylogenetically oldest portion of the brain. It is grossly subdivided into the medulla oblongata (usually called simply the medulla), pons, and midbrain (or mesencephalon). The medulla is the rostral continuation of the spinal cord, while the midbrain lies just below the diencephalon; the pons is the middle portion of the brainstem. Ten of the 12 pairs of cranial nerves (CN III–XII) exit from the brainstem and are primarily responsible for the innervation of the head and neck. CN I (the olfactory nerve) is the initial segment of the olfactory pathway; CN II (the optic nerve) is, in fact, not a peripheral nerve at all, but rather a tract of the central nervous system.

The brainstem contains a large number of fiber pathways, including all of the ascending and descending pathways linking the brain with the periphery. Some of these pathways cross the midline as they pass through the brainstem, and some of them form synapses in it before continuing along their path. The brainstem also contains many nuclei, including: the nuclei of cranial nerves III through XII; the red nucleus and substantia nigra of the midbrain, the pontine nuclei, and the olivary nuclei of the medulla, all of which play an important role in motor regulatory circuits; and the nuclei of the quadrigeminal plate of the midbrain, which are important relay stations in the visual and auditory pathways. Furthermore, practically the entire brainstem is permeated by a diffuse network of more or less “densely packed” neurons (the reticular formation), which contains the essential autonomic regulatory centers for many vital bodily functions, including cardiac activity, circulation, and respiration. The reticular formation also sends activating impulses to the cerebral cortex that are necessary for the maintenance of consciousness. Descending pathways from the reticular formation influence the activity of the spinal motor neurons.

Because the brainstem contains so many different nuclei and nerve pathways in such a compact space, even a small lesion within it can produce neurological deficits of several different types occurring simultaneously (as in the various brainstem vascular syndromes). A relatively common brainstem finding is so-called crossed paralysis or alternating hemiplegia, in which cranial nerve deficits ipsilateral to the lesion are seen in combination with paralysis of the contralateral half of the body.

In general, cranial nerve deficits can be classified as: supranuclear, i.e., caused by a lesion in a descending pathway from higher centers, usually the cerebral cortex, which terminates in the corresponding cranial nerve nucleus in the brainstem; nuclear, if the lesion is in the cranial nerve nucleus itself; fascicular, if the lesion involves nerve root fibers before their exit from the brainstem; or peripheral, if the lesion involves the cranial nerve proper after its exit from the brainstem. The type of deficit produced depends on the site of the lesion.