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Brainstem - want to learn more about it?

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The brain stem is a vital structure for our basic survival. It is composed of three parts, the midbrain, pons, and medulla oblongata and the entire brainstem sits on the clivus, a shallow depression of the skull .

It contains key centres that enable us to breath and our hearts to beat. The structure also gives rise to the majority of the cranial nerves; structures that innervate our entire body to provide sensation, motor, and autonomic function.

This article will discuss the components of the brainstem, their function, as well as the clinical relevance associated with brainstem injury.

Key facts about the brainstem
Location Clivus (the upward sloping segment of bone that leads down to the foramen magnum and up to the posterior clinoid processes of the sphenoid bone)

Traversed by the cerebral aqueduct

Contains the tectum - contains the superior and inferior colliculi

Interpeduncular fossa on its anterior aspect - separates the cerebral peduncles

Contains the red nucleus - origin of the rubrospinal tract which mediates arm swinging 


Basilar portion - contains/transmits the basilar artery, corticospinal tract, corticonuclear fibers, pontine nuclei

Tegmentum - contains the pontine reticular formation, some cranial nerve nuclei, ascending spinal tracts, loci coerulei 

Medulla oblongata

Basilar portion - contains the pyramids (transmit the corticospinal tracts), olives (transmit the olivo-cerebellar tract)

Tegmentum - contains the gracile and cuneate tubercles (and tracts), medullary reticular formation, certain cranial nerve nuclei, ascending spinal cord tracts

Clinical aspects

Brainstem stroke results in paralysis of facial and body muscles. A total locked-in syndrome is also possible. 

Herniation (coning) through the foramen magnum, often as a result of increased intracranial pressure

Components and functions

The brainstem sits on the clivus (the upward sloping segment of bone that leads down to the foramen magnum and up to the posterior clinoid processes of the sphenoid bone). It is composed of the midbrain, pons and medulla oblongata, which are closely related to the overlying cerebellum. Just superior to the midbrain we find the cerebral peduncles that connect it to the cerebral cortex.

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Brainstem and related structures.


This is the most rostral component of the brainstem which is traversed by cerebral aqueduct that connects the third ventricle above to the fourth ventricle below.

An imaginary horizontal line that passes through the aqueduct, divides the midbrain into two parts: one anterior and one posterior.

The posterior one is called tectum. The tectum is therefore known as the ‘roof’ of the midbrain. It has four small surface swellings known as superior and inferior colliculi.

The anterior part is known as the tegmentum. This is formed mainly by the two cerebral peduncles which contain the large ascending (sensory) and descending (motor) nerve tracts, that run to and from the cerebrum from the pons. Between the two peduncles, there is a deep depression the interpeduncular fossa. 

Overview of the brainstem & cerebellum - dorsal view


The tectum has four elevations known as the colliculi. These are visible as 4 small rounded projections on the posterior aspect of the midbrain. The superior colliculi are associated with visual responses and give rise to many tracts including tectospinal and tectobulbar tracts that are responsible for neck, head and eye movements which engage during our orientation reflexes e.g. reflex tuning of our head towards an unexpected stimulus. They are integral to the reflex saccades of eye movements. The inferior colliculi are smaller and associated with auditory paths, it is part of a complicated pathway that connects the cochlea and the primary auditory cortex.

Cerebral Peduncles

If viewed from the front, the cerebral peduncles appear similar to two roman pillars, which are separated by the interpeduncular fossa. If a transverse slice is taken through the midbrain at this level, we can see the deeply pigmented substantia nigra (from the Latin word ‘nigra’ meaning black). This region is responsible for the generation of dopamine that is integral to the basal ganglia via the nigrostriatal tract.

There is also a tiny ventral tegmental area that provides the ventral striatum with dopamine. This is not visible with the naked eye. The tegmentum is just posterior to the substantia nigra. Anterior to the substantia nigra we have the crus cerebri. These transmit the primary motor pathway axons that originate from the cerebral cortex and enter the spinal cord to form the corticospinal tract. The other tracts it contains are corticonuclear and corticopontine fibres.

The red nucleus gives rise to the rubrospinal tract, which is an accessory motor pathway and mediates swinging of the arms in adults and crawling in babies. The oculomotor and trochlear nuclei also reside here, and are connected by the medial longitudinal fasciculus.


In between the midbrain and the medulla is the pons. The pons is a pronounced round projection on the anterior surface of the brain stem. The pons can be seen to bridge the cerebellar hemispheres when viewed from the front.

Want to test yourself on what you've learned? We've got loads of quizzes and free labeling diagrams available on the parts of the brain.

Basilar portion

The anterior two thirds of the pons is referred to as the basilar pons. The basilar groove sits in the midline, and lodges the basilar artery with middle cerebellar peduncle. One of its functions is to transmit bundles of the corticospinal tract that has descended down from the primary motor strip of the cerebral cortex, and connects to the spinal cord accompanied by corticonuclear fibres. This region of the pons also contains the pontine nuclei, which give rise to the axons that transmit to the opposing cerebellar hemisphere, and do this via the middle cerebellar peduncle (via the transverse pontine fibres).

Pontine Tegmentum

The posterior part of the pons is known as the tegmentum. The dorsal surface of this region forms the floor of the fourth ventricle. The superior cerebellar peduncle consists mainly of efferent fibers from the cerebellum to the thalamus. Within the tegmentum we find the pontine reticular formation, and alongside several cranial nerve nuclei and ascending spinal tracts.

The loci coerulei (singular: locus coerulus), are also located in the rostral pons, and lie deep to the floor of the fourth ventricle bilaterally. These deep blue-pigmented nuclei produce and diffuse noradrenaline. The trigeminal nerve originates from the pons and has three divisions (V1, oplthalmic, V2, maxillary, V3- Mandibular).

Medulla Oblongata

This is the inferior most segment and is arguably one of the most vital. It is continuous with the spinal cord at the level of the foramen magnum.

Basilar portion

The anterior medulla contains the pyramids on either side of anterior median fissure. These transmit the corticospinal tract. The olives can be found in the superior medulla lateral to the pyramid, and send an ascending pathway to the opposite cerebellar lobe through inferior cerebellar peduncle. This ‘olivo-cerebellar’ pathway contributes to motor learning via a feed forward system. The olives also have a role to play in sound localization and volume.

Medullary tegmentum

The posterior surface contains the posterior median sulcus, posterolateral sulcus, gracile and cuneate tubercle along with their nuclei. It contains the medullary reticular formation, and also the cranial nerve nuclei and a number of ascending tracts. This is also the precise location of the ‘vital centres’ of cardiorespiratory function and airway protective reflexes (cough, gag). The respiratory centres and cardiac contraction originate from the medulla.

The fourth ventricle is connected by the cerebral aqueduct to the third ventricle above. It lies in the upper part of the medulla.

Medulla oblongata (vagus nerve level) - transverse section

Cranial Nerves

All of the cranial nerves arise from nuclei, most of which are located in the brainstem. All the nerves are bilateral and have a range of functions.

Nuclei Locations:

I- Olfactory- Located in the olfactory bulb.

II- Optic- Located in the lateral geniculate nucleus of the thalamus.

III- Oculomotor- Parasympathetic originates from the Edinger Westphal nucleus, which is located close to the oculomotor nuclei in the midbrain.

IV- Trochlear- Trochlear nucleus located at the level of inferior colliculi.

V- Trigeminal- Motor nucleus located inside the mid pons. Chief sensory is located in the caudal pons, mesencephalic nuclei is present in the midbrain and spinal trigeminal nucleus is in the medulla

VI- Abducens- Abducens nucleus located just deep to the fourth ventricle.

VII- Facial- The fibres loop over the Abducens’ fibres in a cross section of the pontine tegmentum. Taste fibres originate from the solitary tract of the medulla and also synapse in the solitary nucleus. The facial motor nucleus, superior salivatory nucleus and solitary nucleus also project fibres to the facial nerve.

VIII- Vestibulocochlear- Vestibular and cochlear nuclei. Spinal trigeminal nucleus and dorsal nucleus of the vagus nerve. Responsible for hearing and balance.

IX- Glossopharyngeal- Solitary nucleus. Motor (stylopharyngeus only) originates from the nucleus ambiguus. Also synapses in three other nuclei.

X- Vagus- Four separate nuclei. Nucleus ambiguus, solitary nucleus and others.

XI- Accessory- Originates in the cervical spinal cord.

XII- Hypoglossal- Hypoglossal nucleus, which extends the length of the medulla and lies close to the midline.

Study Tip!

One trick for learning the cranial nerve locations is the 4-4 rule. That is to say, the bottom four brainstem nuclei (12,11, 10, and 9) sit in the medulla, while the next four (8, 7, 6, 5) are in the pons. There is a set of interconnected nuclei scattered throughout the brainstem called the reticular formation. They play a crucial role in maintaining arousal and consciousness.

Clinical Notes

Locked in syndrome

A stroke involving the brainstem is likely to result in complete paralysis of facial and body muscles. In total locked in syndrome the eye muscles are also paralyzed.

Brain stem herniation (Coning)

The cranium is a closed cavity. In cases of raised intracranial pressure, the brainstem can herniate through the foramen magnum, which compresses the vital respiratory and circulatory centres of the medulla. This is lethal if prolonged, so urgent surgical decompression is required. This can be achieved by drilling burr holes in the patient skull, or trepanning (removing segments of the skull to relieve pressure).

Arnold Chiari Malformation

This is a congenital defect involving a downward displacement of the cerebellar tonsils through the foramen magnum. It can cause hydrocephalus due to obstruction of CSF flow.

Brainstem - want to learn more about it?

Our engaging videos, interactive quizzes, in-depth articles and HD atlas are here to get you top results faster.

Sign up for your free Kenhub account today and join over 1,085,732 successful anatomy students.

“I would honestly say that Kenhub cut my study time in half.” – Read more. Kim Bengochea Kim Bengochea, Regis University, Denver

Show references


  • Frank H.Netter MD: Atlas of Human Anatomy, 5th Edition, Elsevier Saunders, Chapter 1 Head and Neck.
  • Chummy S.Sinnatamby: Last’s Anatomy Regional and Applied, 12th Edition, Churchill Livingstone Elsevier.
  • Richard L. Drake, A. Wayne Vogl, Adam. W.M. Mitchell: Gray’s Anatomy for Students, 2nd Edition, Churchill Livingstone Elsevier.
  • Elliiot L.Manchell: Gray's Clinical Neuroanatomy: The Anatomic Basis for Clinical Neuroscience.
  • Laureys S, Pellas F, Van Eeckhout P et al. The locked-in syndrome : what is it like to be conscious but paralyzed and voiceless? Prog Brain Res. 2005;150:495-511.

Author, Review and Layout:

  • Shahab Shahid
  • Uruj Zehra 
  • Catarina Chaves


  • Midbrain - midsagittal section - Paul Kim
  • Overview of brainstem & cerebellum - dorsal view - Paul Kim
  • Red nucleus - midsagittal section - Paul Kim
  • Pons - midsagittal section - Paul Kim
  • Medulla oblongata- midsagittal section - Paul Kim
  • Medulla (vagus nerve level) - transverse section of medulla - Paul Kim
  • Cranial nerve nuclei - midsagittal section of brainstem - Paul Kim
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