Put your finger in your ear

like you are pretending to shoot yourself in the head with a finger gun. You are now pointing directly at your brainstem. The brainstem is the gateway that stands between the brain and the rest of the body. It has sensory channels that bring information up from the peripheral nervous system and the spinal cord into the brain for processing. It also has motor channels that carry control instructions from the brain down to the spinal cord, which conveys them on through the peripheral nervous system to the muscles and organs of the body.

The brainstem is thus like a two-way funnel. It collects the all the output from most of the cranial nerves and the spinal cord and dispatches their signals to inform the relevant parts of the brain about the body and its environment. It also collects the processing output from all the parts of the brain and dispatches that output in the other direction to control the body.

The Great Spine-Brain Morph

A number of important structural transitions between the spinal cord and brain take place in the brainstem. One is the reversal in location of white matter and gray matter. The white matter of the spinal cord is on the outside and the gray matter is on the inside. Beginning at the brainstem, the white matter is inside, covered by gray matter on the outside, just as it is in the higher brain. Another change is that the sensory and motor nerve tracts that continue on from the spinal cord switch sides to become contralateral as they ascend to the brain (i.e., the nerve bundles for the left side of the body are on the right side of the brainstem and those for the right side of the body are on the left, again as they are in the brain). Another transition is toward complexity. While the spinal cord is much like an information expressway, with lanes (tracts of nerve fibers) that simply transport signals for the most part, the brain stem is like a highly complex interchange of highways that branch off from many of the spinal cord tracts, although some of the tracts pass on through the brainstem to connect directly with other subcortical structures of the brain.

Lizard Brain and Brain Master

The brainstem is much more than a complex interchange of nerve fibers, though. It is the site of several very basic unconscious body control functions, including breathing, the circulatory system, hunger, digestion and reflexive actions such as gagging, coughing and vomiting (the homeostatic functions). It is also the seat of basic control over consciousness, arousal (the degree to which the brain and body are awake) and emotion. That control is effected mainly by the production of chemicals that affect brain activity (neuromodulators) such as norepinephrine, seratonin and dopamine. The brainstem can be likened to a mindless mini-brain of sorts, a 'lizard brain' that modulates the higher brain in addition to controlling basic body functions directly. One thing that strikes even the naive thinker is the thick connections from the pons to the cerebellum, which is a massive brain structure that is devoted pretty much to keeping body balance and controlling fast, habitual, subconscious body movements and dealing with objects in the spatial dimensions. When you catch a ball or ride a motorcycle in a motocross race, it's your cerebellum that does all the heavy computation and coordination of muscular movement, and it controls the body directly through spinal cord via the brainstem. The cerebral cortex is there mostly as an observer in this activity, and everything happens so fast that our conscious self can barely keep up with it.

Functional Anatomy

The brainstem comprises the medulla, the pons and the midbrain.

The medulla (medulla oblongata) is the lowest part; it connects directly to the spinal cord. The nerve bundles that control muscles cross over here to become contralateral. Centers for control of breathing, the heart, blood vessel constriction, coughing, gagging, swallowing and vomiting lie in the medulla. It also contains a large part of the reticular formation, which modulates wakefulness. Cranial nerves related to the mouth, throat, heart, lungs, and stomach (CN IX, X, XI and XII) enter the brainstem here.

The pons lies just above the medulla. It gets its name, which means 'bridge', from the way it serves as a kind of Y-shaped bridge that connects the higher brain, the medulla and the cerebellum. The pons is tightly associated with the cerebellum. In addition to serving as a kind of highway interchange for nerve fibers from the brain and spinal chord, the pons also cross-connects the two hemispheres of the cerebellum and helps coordinate movements by the two sides of the body. Part of the reticular formation, which controls the levels of consciousness and sleep, also resides in this part of the brain stem. The pons receives cranial nerves related to the skin and muscles of the face and eyes (CN V, VI, VII and VIII).

The midbrain connects the brainstem to the higher brain, specifically the sub-cerebral structures like the thalamus and the cerebral hemispheres. It contains centers for pain, temperature sensing, auditory reflexes, touch and reflexive eye movements. It is also involved in controlling movement. The midbrain receives the cranial nerves for eye movement (CN III and CN IV).

Injury and disease

The brainstem is well-protected within the posterior fossa of the cranium and much of it is surrounded by other brain tissues, so it is not as susceptible to direct injury from trauma as is the spinal cord. It is, however,  susceptible to many kinds of disease,  including stroke (ischemia), infection and cancerous tumors.

Because it is the crux of the nervous system and the basic regulator of body functions, any disease or injury to the brainstem has profound effect on the person or animal. The location and extent of damage from infection or tumor determines the effects and symptoms.

A few of the major syndromes that accompany brain stem damage are listed below.

  • midbrain: Weber's syndrome (light paralysis of left or right side of body, paralysis of opposite-side eye muscles), Benedikt's syndrome (loss of coordination in left or right side of body with partial paralysis of opposite side eye muscles)
  • pons: locked-in syndrome (stroke damage to the downward nerve tracts causes complete paralysis (quadraplegia), including all of the muscles of the face and head except the eye muscles), coma (damage to the reticular formation by disease, stroke or bleeding)
  • medulla: Wallenberg syndrome (loss of pain and temperature senses below the neck on the opposite body side; may also affect sensation in the same-side face, as well as same-side body weakness)


Autopsy studies have linked structural abnormalities of the brainstem to autism. Three clear and specific abnormalities are:

  1. The brainstem is shorter, like a section in the middle was cut out.
  2. The superior olive is pretty much absent.
  3. The facial nucleus is smaller.

These are developmental problems that occur very early in fetal development, at around five weeks, when the nerve tube is forming. The results of those studies, while still few, tend to reinforce the results of studies on ABR and autism. Although brainstem abnormalities are not likely to be 'the cause of autism,' they do suggest physiological explanations for certain aspects of the disorder.

BS and cerebellum

Situation relative to the rest of the brain and interesting facts about autism (image)

Brainstem abnormalities and autism

Brainstem processing and autism

Some processing centers in the brainstem

Superior olive

Induced agenisis of superior olive

ABR and autism

Pupil reflex and heart rate

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