Brain stem
The brain stem is the lower part of the brain, adjoining and structurally continuous with the spinal cord. Most sources consider the pons, medulla oblongata, and midbrain all to be part of the brainstem.
Differentiation of the brain stem from the cerebrum is complex, with regard to both anatomy and taxonomy. Some taxonomies describe the brain stem as the medulla and mesencephalon, whereas others include diencephalic regions.

# General anatomy

## Ventral view/medulla and pons
The most medial part of the medulla is the anterior median fissure.  Moving laterally on each side are the pyramids.  The pyramids contain the fibers of the corticospinal tract, or the upper motor neuronal axons as they head inferiorly to synapse on lower motor neuronal cell bodies within the ventral horn of the spinal cord.
The anterolateral sulcus is lateral to the pyramids.  Emerging from the anterolateral sulci are the hypoglossal nerve (CN XII) rootlets.  Lateral to these rootlets and the anterolateral sulci are the olives. The olives are swellings in the medulla containing underlying inferior olivary nuclei (containing various nuclei and afferent fibers).
Lateral (and dorsal) to the olives are the rootlets for cranial nerves IX and X (glossopharyngeal and vagus, respectively).  The pyramids end at the pontomedullary junction, noted most obviously by the large basal pons.  Between the basal pons, cranial nerve 6, 7 and 8 emerge (medial to lateral).  These cranial nerves are the abducens nerve, facial nerve and the vestibulocochlear nerve, respectively.  At the level of the midpons, the large trigeminal nerve, CN V, emerges.  At the rostral pons, the occulomotor nerve emerges at the midline. Laterally, the trochlear nerve has emerged after emerging out of the dorsal rostral pons and wrapping around to the anterior.

## Dorsal view/medulla and pons
The most medial part of the medulla is the posterior median fissure.  Moving laterally on each side is the fasciculus gracilis, and lateral to that is the fasciculus cuneatus.  Superior to each of these, and directly inferior to the obex, are the gracile tubercles and cuteanus tubercles, respectively.  Underlying these are their respective nuclei.  The obex marks the end of the 4th ventricle and the beginning of the central canal.  The posterior intermediate sulci separates the fasciculi gracilis from the fasciculi cuneatus.  Lateral to the fasciculi cuneatus is the lateral funiculus.
Superior to the obex is the floor of the 4th ventricle.  In the floor of the 4th ventricle, various nuclei can be visualized by the small bumps that they make in the overlying tissue.  In the midline and directly superior to the obex is the vagal trigone and superior to that it the hypoglossal trigone.  Underlying each of these are motor nuclei for the respective cranial nerves.  Superior to these trigones are fibers running laterally in both directions. These fibers are known collectively as the striae medullares.
Continuing in a rostral direction, the large bumps are called the facial colliculi.  Each facial colliculus, contrary to their names, do not contain the facial nerve nuclei.  Instead, they have facial nerve axons traversing superficial to underlying abducens (CN VI) nuclei.  Lateral to all these bumps previously discussed is an indented line, or sulcus that runs rostrally, and is known as the sulcus limitans.  This separates the medial motor neurons from the lateral sensory neurons.  Lateral to the sulcus limitans is the area collectively known as the vestibular area, which is involved in special sensation.
Moving rostrally, the inferior, middle, and superior cerebellar peduncles are found connecting the midbrain to the cerebellum.  Directly rostral to the superior cerebellar peduncle, there is the superior medullary velum and then the two trochlear nerves.  This marks the end of the pons as the inferior colliculus is directly rostral and marks the caudal midbrain.
Spinal Cord to Medulla Transitional Landmark: From a ventral view, there can be seen a decussation of fibers between the two pyramids.  This decussation marks the transition from medulla to spinal cord.  Superior to the decussation is the medulla and inferior to it is the spinal cord.

## Midbrain
The midbrain is divided into three parts.  The first is the tectum, which is "roof" in Latin.  The tectum includes the superior and inferior colliculi and is the dorsal covering of the cerebral aqueduct.  The inferior colliculus, involved in the special sense of hearing sends its inferior brachium to the medial geniculate body of the diencephalon.  Superior to the inferior colliculus, the superior colliculus marks the rostral midbrain.  It is involved in the special sense of vision and sends its superior brachium to the lateral geniculate body of the diencephalon.  The second part is the tegmentum and is ventral to the cerebral aqueduct.  Several nuclei, tracts and the reticular formation is contained here.  Last, the ventral side is comprised of paired cerebral peduncles.  These transmit axons of upper motor neurons.

## Midbrain internal structures
Periaqueductal Gray:  The area around the cerebral aqueduct, which contains various neurons involved in the pain desensitization pathway.  Neurons synapse here and, when stimulated, cause activation of neurons in the raphe nucleus magnus, which then project down into the dorsal horn of the spinal cord and prevent pain sensation transmission.
Occulomotor nerve nucleus:  This is the nucleus of CN III.
Trochlear nerve nucleus:  This is the nucleus of CN IV.
Red Nucleus:  This is a motor nucleus that sends a descending tract to the lower motor neurons.
Substantia nigra:  This is a concentration of neurons in the ventral portion of the midbrain that uses dopamine as its neurotransmitter and is involved in both motor function and emotion.  Its dysfunction is implicated in Parkinson's Disease.
Reticular formation:  This is a large area in the midbrain that is involved in various important functions of the midbrain.  In particular, it contains lowermotor neurons, is involved in the pain desensitization pathway, is involved in the arousal and consciousness systems, and contains the locus ceruleus, which is involved in intensive alertness modulation and in autonomic reflexes.
Central tegmental tract:  Directly anterior to the floor of the 4th ventricle, this is a pathway by which many tracts project up to the cortex and down to the spinal cord.

# Embryology
The adult human brainstem emerges from two of the three primary vesicles formed of the neural tube.  The mesencephalon is the second of the three primary vesicles, and does not further differentiate into a secondary vesicle.  This will become the midbrain.  The third primary vesicle, the rhombencephalon, will further differentiate into two secondary vesicles, the metencephalon and the myelencephalon.  The metencephalon will become the cerebellum and the pons.  The myelencephalon will become the medulla.

# Physiology
There are three main functions of the brainstem.  The first is its role in conduit functions.  That is, all information related from the body to the cerebrum and cerebellum and vice versa, must traverse the brain stem.  The ascending pathways coming from the body to the brain are the sensory pathways, and include the spinothalamic tract for pain and temperature sensation and the dorsal column, fasciculus gracilis, and cuneatus for touch, proprioception, and pressure sensation (both of the body).
The facial sensations have similar pathways, and will travel in the spinothalamic tract and the medial lemniscus also).  Descending tracts are upper motor neurons destined to synapse on lower motor neurons in the ventral horn and intermediate horn of the spinal cord.  In addition, there are upper motor neurons that originate in the brainstem's vestibular, red, tactile, and reticular nuclei, which also descend and synapse in the spinal cord.
Second, the cranial nerves 3-12 emerge from the brain stem.  Third, the brain stem has integrative functions (it is involved in cardiovascular system control, respiratory control, pain sensitivity control, alertness, and consciousness).  Thus, brain stem damage is a very serious and often life-threatening problem.
The practical results of an improperly functioning brainstem are not just related to physical injury.  Behavioral and physical signs can also manifest when there is incomplete pons or mid brain development. Such underdevelopment can affect behavior, academic performance, coordination, anxiety, speech, and focus. Habilitation, the process of first occurrence rehabilitation, makes use of programmatic exercise with the goals of completing development through inducement of neural plasticity

# Physical signs of brainstem disease
Diseases of the brainstem can result to abnormalities in the function of cranial nerves, which may lead to visual disturbances, pupil abnormalities, changes in sensation, muscle weakness, hearing problems, vertigo, swallowing and speech difficulty, voice change, and co-ordination problems. Less obvious cases may complain of poor reading comprehension, lack of focus, altered vigilance, clumsiness, or poor social skills.  Often physical signs to an untrained examiner are not obvious as challenge testing (to reduce cortical compensations) are required during examination. Localizing neurological lesions in the brainstem may be very precise with imaging studies, although the clinical utility of such localization relies upon a clear understanding of brainstem anatomical structures on their functions.

# Physical rehabilitation of brainstem disease
While rehabilitation of brainstem disorders has traditionally belonged to the domain of physiatry or neurology more recently publicly accessible programs have become available that incorporate concepts which promote neural plasticity. 
At least one hospital system, Bon Sequours, St. Francis in Greenville, SC, has incorporated a movement based restorative therapy programs that focus on brainstem neuroplasticity for the treatment of common conditions such as Fibromyalgia.