The cranial nerve nuclei schematically represented; dorsal view. Motor nuclei in red; sensory in blue. (The olfactory and optic centers are not represented.)
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As well as the visible nerves outside of the brain, most of the cranial nerves have associated nuclei within the brainstem. These nuclei are areas of grey matter, and damage to them can have a similar affect to the severing of an actual nerve. Axons to (and from) cranial nerves synapse first at the nuclei.
Just as grey matter in the ventral (closer to front of a human) spinal cord tends to be efferent (motor) fibers, and the dorsal horn tends to contain sensory neurons, nuclei in the brainstem are arranged in an analogous way.
Close to the midline are the motor efferent nuclei, such as the oculomotor nucleus, which control skeletal muscle. Just lateral to this are the autonomic (or visceral) afferent nuclei.
There is a separation, called the sulcus limitans, and lateral to this are the sensory nuclei. Near the sulcus limitans are the visceral afferent nuclei, namely the solitary tract nucleus.
More lateral, but also less posterior, are the general somatic afferent nuclei. This is the trigeminal nucleus. Back at the dorsal surface of the brainstem, and more lateral are the special somatic afferents, this handles sensation such as balance.
Another area, not on the dorsum of the brainstem, is where the branchial efferent nuclei reside. These formed from the branchial arches, in the embryo. This area is a bit below the autonomic motor nuclei, and includes the nucleus ambiguus, facial nerve nucleus, as well as the motor part of the trigeminal nerve nucleus.
Examples of nuclei
There are several cranial nerve nuclei (roman numeral refers to the cranial nerve number):
