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The brainstem (brain stem) is the distal part of the brain that is made up of the midbrain, pons, and medulla oblongata. Each of the three components has its own unique structure and function. Together, they help to regulate breathing, heart rate, blood pressure, and several other important functions. All of these brainstem functions are enabled because of its unique anatomy; since the brainstem houses cranial nerve nuclei and is a passageway for many important neural pathways. This article will discuss the brainstem anatomy in a student-friendly mode and help you ace your neuroanatomy exams.

The goal of this article is to give an overview of the brainstem and the different parts that make it up. Further discussion about brainstem function will also be explored. 

Key facts about the brainstem
Parts Medulla oblongata 
Medulla oblongata Basilar portion - contains the pyramids (transmit the corticospinal tracts), olives (contain inferior olivary nucleus)
Medullary tegmentum - contains the gracile and cuneate tubercles (and tracts), four cranial nerve nuclei
Pons Basilar portion - accommodates the basilar artery, corticospinal tract, corticonuclear fibers, pontine nuclei
Pontine tegmentum - contains the pontine reticular formation, four cranial nerve nuclei, ascending spinal tracts, loci coerulei
Midbrain Traversed by the cerebral aqueduct
Contains the quadrigeminal plate (superior and inferior colliculi)
Cerebral peduncles separated into crura cerebri and tegmentum
Tectum – posterior to the cerebral aqueduct 
Ventricles and cisterns Fourth ventricle and the foramina of Luschka and Magendie
Interpeduncular, Quadrigeminal, Pontine, and Cerebellomedullary cisterns
Function Regulate breathing, heart rate, blood pressure, consciousness, audio-visual reflexes, taste and digestion, autonomic regulation, balance and coordination
  1. Parts
  2. Medulla oblongata
    1. Surface anatomy
    2. Cross-section
  3. Pons
    1. Surface anatomy
    2. Cross-section
  4. Midbrain
    1. Surface anatomy
    2. Cross-section
  5. Reticular formation
  6. Function
  7. Related content
  8. Clinical notes
    1. Locked in syndrome
    2. Brain stem herniation (coning)
    3. Arnold Chiari malformation
  9. Sources
+ Show all


In the plant world, most flowers are connected to the tree by a stem or stalk. Similarly, the majority of brain tissue is connected to the rest of the body via the brainstem. The brainstem is a stalk-like projection extending caudally from the base of the cerebrum. It facilitates communication between the cerebrum, cerebellum, and spinal cord

The brainstem begins at the level of the cerebral peduncles (anteriorly) and the corpora quadrigemina or quadrigeminal plate (posteriorly) or tectal plate. It continues along a slight posteroinferior course until it ends at the decussation of the pyramids (at the level of the foramen magnum of the skull). 

The brainstem is widest at its proximal end and becomes narrower toward the distal end. There are three parts of the brainstem:

  • the medulla oblongata is the narrowest and most distal part
  • the pons lies anteriorly and in the middle segment of the brainstem
  • and the midbrain is the widest and most superior segment.

The brainstem is be divided horizontally (as above) and vertically. Most textbooks divide the midbrain into tectum and tegmentum, but the division is actually extended caudally into other brainstem segments. The tectum (Latin word for roof) and tegmentum (Latin word for covering) are used in relation to the developing central cavity of the neural tube

The tectum is the roof of the cavity while the tegmentum forms the ventral covering. The central cavity of the neural tube becomes the aqueduct of Sylvius, the fourth ventricle, and the central canal of the spinal cord. Therefore the tectum is the area dorsal to the aqueduct of Sylvius (in the midbrain) and fourth ventricle (at the pons); while the tegmentum is ventral to these structures at the respective levels. 

However, the crus cerebri and basilar pons (described below) are not considered as part of the tegmentum. This is because both structures are not a part of the primitive neural tube, but develop later in the embryological timeline. As a result, they are considered and discussed as separate entities from the tectum and tegmentum.

Each part has unique gross anatomical features and houses special nuclei that are important for daily functions. Some of these nuclei and tracts traverse more than one part of the brainstem and therefore may be mentioned in more than one section of this article. There are also several important structures surrounding the brainstem that tend to pop up in anatomy quizzes and exams. Those structures will be discussed here as well. 

It is easier to discuss the brainstem in a caudocranial approach, as the lower portion has fewer structures to recall compared to the proximal part of the brainstem. Therefore, the discussion will begin with the medulla oblongata.

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Medulla oblongata

The medulla oblongata or medulla is the narrowest and most caudal part of the brainstem. It is a funnel-like structure that extends from the decussation of the great pyramids, passes through the foramen magnum (which is the largest of all the foramina and fissures of the skull), to the inferior pontine sulcus (pontomedullary groove). As the medulla continues upward in the posterior cranial fossa, it terminates at the inferior pontine sulcus (anteriorly) and the medullary striae of the fourth ventricle (posteriorly). 

At the upper posterior surface of the medulla, there is the fourth ventricle, the floor of which is called rhomboid fossa. The rhomboid fossa does not extend throughout the whole length of the medulla. It is divided into two parts based on whether or not the fossa is present at a level: 

  • There is an upper, rostral or open part where the dorsal surface of the medulla is formed by the rhomboid fossa.
  • Also, there is a lower, caudal or closed part where the fourth ventricle has narrowed at the obex in the caudal medulla and surrounds part of the central canal.

The medulla develops from the myelencephalon, which is a secondary brain vesicle that arises from the rhombencephalon (the hindbrain). The other secondary brain vesicle to arise from the hindbrain is superior to the myelencephalon and gives rise to the pons.

Surface anatomy

Ventral surface

The ventral surface of the medulla is marked by a midline depression known as the anterior median fissure. This is a cranial continuation of the anterior median fissure of the spinal cord, which divides the medulla into symmetrical halves. The most distal end of the anterior median fissure is covered by crisscrossing fibers known as the decussation of the pyramids

The pyramids contain the corticospinal fibers that start from the motor cortex, pass through the internal capsule, and contribute to the formation of the cerebral peduncles. The fibers then descend to the spinal cord, passing through the pons and the medulla. Their role is to regulate muscle movement. Most of these fibers cross to the opposite side at the level of the caudal medulla and they form the aforementioned decussation of pyramids. 

Lateral to the medullary pyramids is a shallow depression that represents the cranial continuation of the ventrolateral sulcus of the spinal cord. It separates the pyramids from another prominent bulge, the olive, which corresponds to the location of the inferior olivary nucleus. Posterolateral to the olives are the inferior cerebellar peduncles. Although these structures lie above the upper limit of the medulla, they are often labeled as medullary structures owing to the fact that they carry fibers from the medulla to the cerebellum.

The lower four cranial nerves also emerge from the anterior surface of the medulla. The hypoglossal nerve (CN XII) rootlets emerge between the pyramids and the olives before they unite to form the trunk of the nerve. The glossopharyngeal nerve (CN IX) rootlets arise between the inferior cerebellar peduncle and the olive (close to the choroid plexus of the fourth ventricle). Caudal to CN IX are the rootlets of the vagus nerve (CN X). The most inferior of the cranial nerves is the accessory nerve (CN XI) whose rootlets ascend the lateral aspect of the medulla to unite as the nerve trunk.

Dorsal surface

The posterior surface of the medulla can be divided into an upper open area and a lower closed area. The open area is also known as the floor of the fourth ventricle or rhomboid fossa. It has unique raised areas that mark the location of underlying structures. These include the hypoglossal and vagal trigones that are present on either side of the posterior (dorsal) median sulcus. The hypoglossal trigone (location of the nucleus of CN XII) is superior to the vagal trigone (location of CN X nucleus). The vagal trigone is above the obex, which is the most caudal aspect of the fourth ventricle. 

The closed part of the posterior surface (outside of the fourth ventricle) of the medulla is also divided into symmetrical halves by the caudal continuation of the dorsal median sulcus. On either side of the sulcus is a raised structure known as the gracile tubercle. Deep to the tubercle is the gracile nucleus, which is the point of termination of the gracile fasciculus of the dorsal column of the spinal cord. 

The paired cuneate tubercles, which are raised areas over the cuneate nucleus also marks the point of termination of the cuneate fasciculus. It is laterally related to the gracile tubercle. The cuneate fasciculus is medially related to the lateral funiculus which carries contralateral corticospinal and spinothalamic tracts. Similarly, the trigeminal tubercle is laterally related to the cuneate tubercle. It represents the location of the spinal nucleus of the trigeminal nerve (CN V).

The inferior cerebellar peduncles also form part of the posterior surface of the medulla. It is best seen when the cerebellum is removed. This paired tract carries efferent and afferent impulses between the cerebellum and vestibular nuclei.

There are unique openings (one on either posterolateral surface and one in the posterior midline) on the medulla that facilitate communication between the fourth ventricle and the surrounding cisterns. Those on the posterolateral surfaces of the medulla are called the lateral apertures of the fourth ventricle (lateral apertures of Luschka). The midline opening is called the median aperture of the fourth ventricle (foramen of Magendie). 

Read more in our study unit and then test how much you know about the subarachnoid cisterns by trying our custom quiz below.


The layout of tracts and nuclei varies from one level of the brainstem to the other. As a result, the cross-sectional layout of the nuclei and tracts within the medulla may be slightly different going from the decussation of the pyramids to the level of the olives, for example.

The two main cross-sectional points that will be discussed in the medulla is at the level of the vagus (CN X) and hypoglossal (CN XII) nerves. Note that the nuclei and tracts that are discussed are paired structures present in both the left and right halves of the brainstem.

The nuclei and tracts at the level of the vagus nerve (CN X) can be grouped according to their position on the cross-sectional view. At the dorsomedial part of the medulla is the inferior olivary nucleus, which is medial to the hypoglossal nucleus. The medial longitudinal fasciculus (MLF) and the raphe nuclei are two other midline tracts that are ventral to the inferior olivary nucleus. The dorsal and medial accessory olivary nuclei are laterally and ventrolaterally related to the raphe nucleus, respectively. The most ventral midline structure at this level is the dense corticospinal tracts that form the pyramidal tract. 

The nuclei at the dorsolateral part of the medulla have (arranged from medial to lateral) the posterior (dorsal) vagal, solitary, medial vestibular, and cuneate nuclei. The cuneate nucleus is situated within the inferior cerebellar peduncle. Both the spinal trigeminal tract and nucleus are ventral to the cuneate nucleus at this level. The lateral aspect of the medulla is occupied by the lateral reticular nucleus. It is ventral to the spinal trigeminal tract and nucleus, lateral to the nucleus ambiguus and dorsal accessory olivary nucleus, and dorsal to the spinothalamic and spinocerebellar tracts. The reticular formation occupies a substantial amount of space in the dorsal half of the medulla. It is surrounded by the midline (medially), dorsomedial, dorsolateral, and lateral groups of nuclei and tracts mentioned above.

The medial lemniscus occupies the ventral midline of the medulla. It is dorsally related to the pyramids and medial to the inferior and medial accessory olivary nuclei.

The nuclei and tracts found at the level of the hypoglossal nucleus (CN XII) can also be grouped based on their position on the cross-sectional view. The nuclei in the dorsomedial group (from medial to lateral) are the hypoglossal, dorsal vagal, the nucleus of the solitary tract, and gracile nuclei. The actual solitary tract is ventrolateral to its nucleus. Note also that the inferior olivary nucleus is no longer visible at this level. The cuneate nucleus is much larger at this level and is still found in the dorsolateral position. The medial longitudinal fasciculus and the medial lemniscus pathway maintain their midline location. The medial lemniscus pathway is the most ventral of the two structures and has the internal arcuate fibers extending laterally from it. 

The spinal trigeminal tract and nucleus are located in the lateral aspect of the medulla at this level. Both structures are found dorsal to the lateral reticular nucleus, which is lateral to the nucleus ambiguus and posterior accessory olivary nucleus. There is a central tegmental tract that separates the lateral reticular nucleus from the olivary nucleus. Both of these structures are located toward the ventrolateral aspect of the medulla. Furthermore, they are medially related to the superficial arcuate fibers. 

The fibers of CN XII leave the medulla between the olivary nucleus and the pyramidal tracts. The pyramidal tracts, along with the arcuate nucleus are found in the ventromedial part of the medulla. The arcuate nucleus is the most ventral of the two structures. 

The table below will provide general information about the nuclei found in the medulla. More information about the ascending and descending tracts can be found here. 

Nuclei of the medulla oblongata
Gracile nucleus Receive sensory input from the lower limbs and lower trunk
Cuneate nucleus Receive sensory input from the upper limbs and neck
Spinal nucleus of trigeminal nerve Receives pain information from CN V, CN VII, CN IX, and CN X
Posterior nucleus of vagus nerve Motor supply to thoracic and abdominal viscera
Nucleus of the accessory nerve Motor innervation to the laryngeal, sternocleidomastoid, and trapezius muscles
Nucleus of hypoglossal nerve Motor innervation to intrinsic and extrinsic tongue muscles (except palatoglossus)
Nucleus ambiguus Special motor innervation to pharyngeal and laryngeal structures
Nuclei of solitary tract Receives special sensory input from the epiglottis, thoracic and abdominal viscera, and the carotid body
Inferior olivary nucleus Receives input from the contralateral dorsal horn of the spinal cord, ipsilateral red nucleus
Arcuate nucleus Receives input from the corticospinal tract and relay them to the cerebellum via the external arcuate fibers. It helps to regulate the respiratory rate.

Now you can reinforce and challenge your memory! Read more about in our articles and then see how many new terms you have added to your anatomy bank by taking these quizzes on the cross-section of the medulla.


The pons is another relatively short segment of the brainstem that resides in the posterior cranial fossa. The roughly 2.5 cm structure rests against the clivus of the skull, below the tentorium cerebelli. The pons develops from the metencephalon, which is a secondary brain vesicle that is formed from the hindbrain (rhombencephalon). The metencephalon is found caudal to the mesencephalon, and cranial to the myelencephalon (medulla). 

Surface anatomy

When viewed from the ventral aspect, the pons resembles a dome-like structure with numerous striations across its surface. It is widest in the middle and tapers toward the lateral extremities. The surface of the pons is otherwise unremarkable, with the exception of a shallow depression that runs along its vertical axis. This is called the basilar groove, which accommodates the basilar artery – a major part of the posterior blood supply of the brain

The function of the pons is to house the pontine nuclei and to facilitate corticopontocerebellar communication. It also enables communication between the left and right hemispheres of the cerebellum. Interestingly enough, it is the corticopontocerebellar fibers that are responsible for the striated appearance of the pons. 

The pons is limited superiorly by the superior pontine sulcus and ends inferiorly at the pontomedullary junction or inferior pontine sulcus. The motor and sensory fibers of the trigeminal nerve (CN V) emerge from the lateral surface of the pons. Additionally, there are three cranial nerves that emerge from the inferior pontine sulcus. These nerves are (listed from medial to lateral) the:

The posterior surface of the pons is formed by the upper part of the rhomboid fossa, which is best appreciated when the cerebellum has been resected. This process reveals the most lateral boundary, which is formed by the middle cerebellar peduncles. These are the largest of the peduncles and contain massive input from the pons to the cerebellum (pontocerebellar fibers). The superior limit of the posterior surface of the pons is the superior medullary velum, while the inferior border is formed by the striae medullaris (fibers of the arcuate nucleus).

A pair of raised bodies known as the medial eminences, separated by a dorsal median sulcus, is the hallmark feature of the posterior surface of the pons. The caudal extent of the medial eminence is slightly more pronounced than the cranial segment of the structure. This portion is called the facial colliculus. It is a result of the presence of the genu of the facial nerve (CN VII), which curves around the nucleus of the abducens nerve (CN VI). On either side of the facial colliculus is another slightly raised area that corresponds to the location of the vestibular nucleus (CN VIII) known as the vestibular area


The pons can be subdivided into ventral (basal) and dorsal (tegmental) portions on the cross-section for easier discussion. The basal pons or basis pontis is the larger of the two parts of the pons. It is made up of corticospinal and corticobulbar tracts traversing a craniocaudal pathway. Additionally, it also has the pontine nuclei and horizontal pontine fibers that eventually form the middle cerebellar peduncle. 

The smaller pontine tegmentum contains the cranial nerve nuclei for CN V - CN VIII as well as several white matter tracts (medial longitudinal fasciculus, medial and lateral lemnisci, and others) and the fourth ventricle.

The table below summarizes the major nuclei found in the pons. For more details regarding the other tracts found in this area, refer to the article on the midbrain and pons.

Nuclei found in the pons
Pontine nuclei Location: throughout the basal pons – numerous nuclei scattered throughout the area
Pontocerebellar fibers help to regulate motor function
Nuclei of trigeminal nerve Location: pontine tegmentum
Motor nucleus – motor innervation to the muscles of mastication, mylohyoid, anterior belly of digastric, tensor tympani muscles
Sensory nucleus – sensory input from the scalp, face, orbit, paranasal sinuses, and general sensory input from the anterior two-thirds of the tongue
Spinal nucleus – discussed above
Nucleus of abducens nerve Location: pontine tegmentum – deep to the facial colliculus, anterolateral to the medial longitudinal fasciculus (in the midline), medial to the vestibular nuclei, and posterior to the medial lemniscus
Innervates the lateral rectus muscle
Motor nucleus of facial nerve Location: pontine tegmentum – anterolateral to the abducens nucleus, posterior to the medial lemniscus, and anteromedial to the vestibular nuclei
The genu of the facial nerve gives rise to the facial colliculus
Innervates the muscles of facial expression
Vestibular nuclei Location: pontine tegmentum – medial, caudal aspect of the superior, and cranial part of the lateral vestibular nuclei are found in the pons
Receives input from the vestibules of the internal ear
Assists in balance and coordination

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The midbrain is the shortest segment of the brainstem. It extends caudally from the base of the thalamus to the superior roof of the fourth ventricle. It passes through an opening in the tentorium cerebelli (an extension of the dura mater). The structure arises from the mesencephalon, which is one of three primary brain vesicles that arise from the cranial part of the closed neural tube (above the fourth pair of somites). The mesencephalon is located between the forebrain (prosencephalon) and hindbrain (rhombencephalon). 

Surface anatomy

The superior boundary of the midbrain is indicated by an imaginary horizontal line extending from the posterior commissure (below the pineal gland and above the superior colliculi) to the mammillary bodies. Inferiorly, the midbrain ends at the superior pontine sulcus (anteriorly) and the superior medullary velum (posteriorly). The superior pontine sulcus is a shallow, horizontal groove between the upper border of the pons and the cerebral peduncles. The superior medullary velum is a thin sheet of neural tissue that forms the roof of the fourth ventricle.

Externally, the midbrain is characterized by two stalks known as the cerebral peduncles (pedunculus cerebri) along the ventral surface. They represent the numerous ascending and descending tracts that connect the cerebral cortex to the pons and spinal cord. There is a relatively shallow depression between the cerebral peduncles known as the interpeduncular fossa. The posterior perforated substance (which accommodates small blood vessels to the midbrain) forms the floor of the fossa. The oculomotor nerve (CN III), the terminal bifurcation of the basilar artery (the posterior cerebral arteries) and the mammillary bodies of the hypothalamus can all be observed in the interpeduncular fossa. The cerebral peduncles then converge toward the midline as they meet the pons. 

On either side of the midbrain, the optic tract course around the lateral surfaces. They eventually terminate at the lateral geniculate body (which is posterolateral to the thalamus). The medial geniculate body and the uncus of the temporal lobe are also laterally related to the midbrain. The posterior surface of the midbrain has two pairs of raised, round protrusions that are known collectively as the corpora quadrigemina (tectal plate or quadrigeminal plate). This complex consists of the superior and inferior colliculi, which house their respective nuclei. Each colliculus is separated from the contralateral counterpart by the frenulum of the superior medullary velum.

The fibers of each trochlear nerve (CN IV) nucleus crosses the midline and emerge on the opposite side of the frenulum of the superior medullary velum, just below the inferior colliculi. The trochlear nerves eventually become inferolaterally, then anteroinferiorly related to the cerebral peduncles as they course around the midbrain on its way to its target organ.

The superior cerebellar peduncles are also considered as part of the midbrain. It is best appreciated when the cerebellum is resected. This paired structure contains mainly cerebellar output and connects the cerebellum with the midbrain (the red nucleus specifically), the thalamus and the motor cortex.


The midbrain cross-section views reveal more information about the structure and organization of this portion of the brain. This brainstem segment is divided into a tectum (Latin word meaning roof), tegmentum (Latin word for covering) and the crus cerebri. 

The tectum is the part of the midbrain that is dorsal to the cerebral aqueduct of Sylvius (a conduit that connects the third and fourth ventricles). The tegmentum, on the other hand, is ventral to the aqueduct of Sylvius. The crus cerebri are large collections of ascending and descending tracts traveling to and from the brain. Each crus is separated from the tegmentum by the substantia nigra. This is a pigmented lamina that is made up of dopaminergic and GABAergic neurons. These are cells that produce specific neurotransmitters for which they are named. It is important to note that while each crus cerebri is separate from each other, the tegmentum is continuous across the midline of the midbrain. Some texts refer to the crus cerebri and tegmentum together as the cerebral peduncles. 

Another prominent structure seen on cross-section is the red nucleus. This is a well-defined collection of cell bodies that appear bright red on a freshly sectioned specimen. The paired structure is located along the midline of the tegmentum, posteromedial to the substantia nigra. Additionally, there is a circumferential area of gray matter surrounding the cerebral aqueduct known as the periaqueductal gray matter. 

There are several important nuclei and tracts located throughout the midbrain. This article will only give an overview of the major nuclei. Further details about the internal composition of the brainstem can be found in articles about the nuclei and tracts of the midbrain and pons.

Nuclei found in the midbrain
Superior colliculi Located in the tectum – deep to the superior colliculi
Communicates with contralateral superior colliculus via its own commissure
Communicates with the lateral geniculate body via the superior brachium
Involved in pupillary and optic reflexes
Nucleus of oculomotor nerve Located in the tegmentum – anterolateral to the cerebral aqueduct
Its fibers pass through the red nucleus and exit the brainstem at the superior pontine sulcus
Motor innervation to all the extraocular muscles (except superior oblique and lateral rectus)
Accessory nuclei of oculomotor nerve (Edinger-Westphal) Located in the tegmentum – Medial to CN III nucleus and anterolateral to the cerebral aqueduct
Fibers accompany those of CN III
Provides parasympathetic innervation to the muscles of the iris
Red nucleus Located in the tegmentum – anterolateral to the CN III nucleus
Participates in the extrapyramidal motor pathway (initiation, selective activation, and coordination of movements)
Inferior colliculi Located in the tectum – deep to the inferior colliculi
Communicates with contralateral inferior colliculus via its own commissure
Communicates with the medial geniculate body via the inferior brachium
Involved in the auditory pathway
Nucleus of trochlear nerve Located in the tegmentum – posteromedial to the medial longitudinal fasciculus
Fibers decussate at the superior medullary velum and travel laterally, then ventrally on the opposite side
Motor innervation to the superior oblique extraocular muscle
Mesencephalic nucleus of trigeminal nerve Located in the tectum – lateral margin of the periaqueductal grey matter; joins the principal sensory nucleus of CN V caudally (deep to the medial eminence)
Fibers exit the brainstem with the sensory division of CN V
Responsible for proprioception

Reticular formation

The reticular formation is a vast network of neurons that are involved in maintaining consciousness and initiating arousal. This neuronal tract extends from the spinal cord to the diencephalon and occupies different parts of the brainstem throughout.

The nuclei of the reticular formation are situated deep within the brainstem along its vertical axis. On each half of the brainstem, there is a lateral, medial, and median group of nuclei. The combined effect of this collection of nuclei are related to the regulation of the circadian rhythm, coordinates the respiratory and antigravity muscles, modifies reflex activity, and also helps to coordinate the muscles of facial expression.


To summarize, there are three basic functions of the brainstem:

  • To act as a conduit for ascending and descending pathways going to and from the brain
  • To house the cranial nerve nuclei
  • To integrate the functions of several vital systems

More specific functions of each part of the brainstem are dependent of the cranial nerve nuclei and tracts that reside in each area. The medulla oblongata controls the respiratory function, cardiovascular system, as well as gastrointestinal and digestive activities. The pons is involved in controlling movements of the body and equilibrium. Finally, the midbrain controls eye movements and integrates it with auditory input. 

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