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Subcortical structures

Recommended video: Hippocampus and fornix [12:00]
Hippocampus, fornix and neighbouring structures.
Subcortical structures (superior view)

If we imagine our brain as a peach, on the cross section of that peach we’d see the outer skin, the flesh and an inner stone. The skin is analogous to the cerebral cortex, the fleshy part is the deep white matter and the stone represents the subcortical structures.

Subcortical structures are a group of diverse neural formations deep within the brain which include the diencephalon, pituitary gland, limbic structures and the basal ganglia. They are involved in complex activities such as memory, emotion, pleasure and hormone production. They act as information hubs of the nervous system, as they relay and modulate information passing to different areas of the brain. This page will introduce you to the core of our brain, embodied in the subcortical structures.

Key facts about the subcortical structures
Definition Islets of gray matter found beneath the cerebral cortex, organized in several distinctive parts of the brain.
Parts Diencephalon, pituitary gland, limbic structures, basal ganglia.
Functions Processing and relaying neural impulses between the different parts of the brain.
  1. Diencephalon
    1. Thalamus
    2. Epithalamus
    3. Subthalamus
    4. Hypothalamus
  2. Pituitary gland
  3. Limbic system
    1. Hippocampus
  4. Basal ganglia
  5. Sources
+ Show all


The diencephalon is the posterior part of the forebrain found deep within the cerebrum. It consists of the thalamus, epithalamus, subthalamus and hypothalamus. Each of these structures have many roles essential for survival and optimal functioning of the human body, so let’s get introduced to their anatomy.


The thalamus is the largest subcortical structure. It acts as a relay center between the brainstem and cerebrum. The thalamus is comprised of 12 nuclei–anatomically, nine of them are grouped into anterior, medial, and lateral nuclei, while the remaining three form laminar sheets that separate these groups. Functionally, they can be classified into three groups: relay nuclei, intralaminar nuclei and the reticular nucleus. 

Two of the lateral thalamic nuclei, the lateral and medial geniculate bodies, are together called the metathalamus. Geniculate bodies are the sensory relay nuclei. The medial geniculate body is an auditory relay station, while the lateral geniculate body is the optic relay station. The thalamic nuclei are in charge of an entire spectrum of body functions, such as relaying sensory and motor signals and regulating consciousness, sleep, and alertness.

Learn all about thalamus anatomy and the auditory and visual pathway with these study units:


The epithalamus is the posterior part of the diencephalon. It is located posteroinferior to the thalamus and consists of the pineal body, stria medullaris and habenular trigone. Historically, the pineal gland was considered to be the third eye because of its connections to the visual system. But we now know that pineal gland function is to control the sleep-wake cycle (circadian rhythm) by releasing the sleeping hormone, melatonin. The pineal gland’s connections with the visual system provide information about the time of the day based on how much light there is. Darkness triggers melatonin secretion. 

The stria medullaris is a bundle of white matter connecting the hypothalamus and habenular trigone. The habenular trigone is a triangular area found in front of the superior colliculus which provides fibers to the pathway connecting the basal ganglia and the ventral brainstem. This pathway enables initiation and control of movements.


Subthalamic nucleus (lateral-left view)

The subthalamus is found ventral to the thalamus. It consists of the subthalamic nucleus, the zona incerta (of Forel) and the peripeduncular nucleus. 

The subthalamic nucleus is functionally part of the basal ganglia, it participates in the control of motor activity. The role of the zona incerta remains unknown. It relays fibers between a wide range of CNS regions, and is thought to play a role in activities such as motor integration and the accuracy of body movements. The peripeduncular nucleus has rich connections with the limbic system and is believed to play an important role in controlling sexual behaviour.

Learn more about the subthalamus anatomy and other diencephalon structures in our study unit.


Inferoanterior to the thalamus is the hypothalamus. It is a part of the diencephalon that maintains endocrine and autonomic functions. By controlling many important mechanisms related to survival, such as food and fluid intake, sleeping, metabolism, and body temperature, the hypothalamus enables a state of physiological equilibrium (body homeostasis). 

Structurally, the hypothalamus is composed of 13 nuclei. Anatomically they are arranged anteroposteriorly into three groups: anterior (preoptic and supraoptic), middle (tuberal), and posterior (mammillary). Hypothalamic nuclei can also be divided in mediolateral zones according to their proximity to the third ventricle:

  • Periventricular – controls the release of hormones from the anterior pituitary lobe
  • Medial – regulates the autonomic nervous system, release of hormones from the posterior pituitary lobe and circadian rhythms 
  • Lateral – controls emotions due to its connections with the limbic system, and regulates feeding and sleep-wakefulness

The hypothalamus controls survival mechanisms through special pathways called the hypothalamic axes. The axes project from the hypothalamus to the pituitary gland, and from the pituitary gland towards target organs. There are three main axes:

  • Hypothalamic-pituitary-adrenal axis mediates the stress response
  • Hypothalamic-pituitary-thyroid axis regulates metabolism intensity
  • Hypothalamic-pituitary-gonadal axis regulates reproduction
Key facts about the hypothalamic axes
Hypothalamic-pituitary-adrenal axis Hypothalamic hormones: corticotropin-releasing hormone (CRH)
Pituitary hormone: adrenocorticotropic hormone (ACTH)
Target: adrenal gland (glucocorticoids, cortisol)
Hypothalamic-pituitary-thyroid axis Hypothalamic hormone: thyrotropin-releasing hormone (TRH)
Pituitary hormone: thyroid-stimulating hormone (TSH)
Target: thyroid gland (thyroxine, triiodothyronine)
Hypothalamic-pituitary-gonadal axis Hypothalamic hormone: gonadotropin-releasing hormone (GRH)
Pituitary hormone: luteinizing hormone (LH), follicle-stimulating hormone FSH)
Target: gonads (estrogen, testosterone)

It’s notable that every axis goes through the pituitary gland (hypophysis). This is because the hypothalamus and pituitary gland are intricately linked. Hypothalamic axons link the hypothalamus with the posterior pituitary whilst a collection of blood vessels called the hypophyseal portal system connects the hypothalamus to the anterior pituitary. 

Hypothalamic axons project from the hypothalamus to the posterior lobe of the pituitary gland (neurohypophysis). These axons transport neurohormones (oxytocin, antidiuretic hormone/vasopressin) produced by the hypothalamus to the neurohypophysis; where they are stored, and released into the circulatory system when needed.

The hypophyseal portal system acts to transport hypothalamic "releasing" hormones to the anterior lobe of the pituitary gland (adenohypophysis). Hypothalamic hormones are synthesized by the hypothalamus and act to control the secretion of hormones, such as thyroid-stimulating hormone and adrenocorticotropic hormone, produced by endocrine cells of the adenohypophysis. This is why the hypothalamus is colloquially referred to as the master of the master, as it both produces hormones itself and also controls the production and release of hormones from the pituitary gland. 

Test your knowledge and consolidate what you've learned about the hypothalamus with the following quiz:

To learn more about this tiny but very important part of the brain, dive into this study material.

Pituitary gland

Let us introduce you to one of the major glands of the human body. The pituitary gland, or hypophysis, is a continuation of the hypothalamus. It is found in the sella turcica of the sphenoid bone

It consists of an anterior lobe (adenohypophysis) and a posterior lobe (neurohypophysis). Upon stimulation by hypothalamic releasing-hormones, the anterior lobe secretes tropic and trophic hormones, such as thyroid stimulating hormone, which regulate the function of other endocrine glands. The posterior lobe stores oxytocin and vasopressin made by the hypothalamus and releases them when needed. 

To learn how this powerful gland affects the entire endocrine profile of the human body, check out our study unit and custom quiz:

Limbic system

The limbic system is an ancient part of the human brain. It is comprised of cortical, subcortical and brainstem areas. On a midsagittal section of the brain, the limbic system extends through the medial aspects of the temporal, frontal, and parietal lobes

The parts of the cerebral cortex involved in limbic function are together called the limbic cortex. The limbic cortex consists of the cingulate gyrus, parahippocampal gyrus, medial orbitofrontal gyri, temporal poles of the hemispheres and the anterior part of the insular cortex.

Deep structures that comprise the limbic system are the hippocampal formation, amygdala, olfactory cortex, diencephalon, basal ganglia, basal forebrain, septal nuclei and brainstem.

The limbic system controls olfaction, memory, emotions and body homeostasis. Concerning emotions, the main amygdala function is responding to fear. Because of the numerous functions of the limbic system, synapses within it are very active (high synaptic plasticity), so it is a region often associated with epilepsy.


The hippocampus is an often used synonym for what is officially called the hippocampal formation in anatomy. It plays an important role in long term memory storage and spatial navigation.

The hippocampal formation continues on the parahippocampal gyrus, as it dives into the medial temporal lobe. The hippocampal formation consists of the dentate gyrus, hippocampus and subiculum. It may sound confusing to say that the hippocampus is part of the hippocampal formation, as we know these terms are often used as synonyms. However, in its narrowest meaning the anatomical term hippocampus actually refers to the part of the hippocampal formation found between the dentate gyrus and subiculum. 

So, the dentate gyrus, hippocampus and subiculum together form the hippocampal formation which is named for its shape, a seahorse. The formation has two parts: head and tail, although some sources describe three parts (head, body and tail). The head refers to the wider anterior part, while the tail continues posteriorly. 

The hippocampal formation communicates with many different parts of the brain through its major output called the fimbria, which later becomes the fornix. The fornix projects from the hippocampus to the mammillary bodies of the hypothalamus. These connections are important for creating long-term memory. If a person had an injury that affected the hippocampus function, they would be unable to create new memories (anterograde amnesia) after their injury.

Find out more about the learning part of the brain with our additional resources:

Basal ganglia

The basal ganglia, or basal nuclei, are a group of interconnected grey matter nuclei found deep within the white matter of the telencephalon, diencephalon and midbrain. They form part of the extrapyramidal motor system and help in fine tuning motor function. 

Basal ganglia are made up of five pairs of nuclei: caudate nucleus, putamen, globus pallidus, substantia nigra and subthalamic nucleus. The substantia nigra and subthalamic nucleus are not anatomical constituents of the basal ganglia, but functionally they belong together. Instead, the substantia nigra is located in the midbrain while the subthalamic nucleus is a part of the subthalamus, which is found in the diencephalon ventral to the thalamus.

The putamen and caudate nucleus together are also known as the striatum and they are separated by a sheet of white matter called internal capsule. The putamen and globus pallidus form the lentiform nucleus

So, what is the point of the basal ganglia? In a nutshell, they send signals to the thalamus which determine how the thalamus will affect the motor cortex. They communicate with the thalamus via three pathways: direct, indirect, and hyperdirect. The direct pathway is excitatory and plays a major role in initiating a voluntary movement, while the indirect pathway is inhibitory and prevents involuntary movements. The hyperdirect pathway is the quickest way to inhibit all motor functions and suppress involuntary movement. 

The importance of the basal ganglia can be appreciated through the most prevalent disease of the extrapyramidal system–Parkinson’s disease. Damage of the direct pathway causes difficulties in initiating movement in people who have this medical condition, while the indirect and hyperdirect pathways cause notable involuntary hand shaking (tremor) since they are not able to suppress them.

To learn more about the basal ganglia, we recommend that you go through our study unit and custom quiz, and you’ll master this topic in no time.

And last but not the least, we encourage you to take our custom quiz about the subcortical structures. With this quiz, you can test your knowledge about all subcortical structures in one place!

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