Sleep and the brain: What’s going on in there?

You put your head on the pillow and, with any luck, you’re soon asleep. 

In what seems like moments later, the hateful din of your morning alarm breaks your slumber. 

Although you’ve been lying there for 7–9 hours, it often feels like nothing more than a blink of an eye. Sleep’s strange, isn’t it? 

We know sleep is vital for good health, but scientists are still figuring out exactly what goes on while we’re snoozing.

Here, we’ll take a look inside the sleeping brain. It’s not quite as peaceful as you might imagine. Although some parts of the brain fall silent, other brain regions are more active when you’re asleep than when you’re awake.

First off, let’s look at the anatomy of sleep.

Sleep phases

There are two main phases: 

  1. Rapid eye movement, or REM sleep, is when you do most of your dreaming.

  2. Non-REM sleep is split into three numbered stages: N1, N2, and N3. 

When you first go to sleep, you enter N1, then progress to the deeper N2. Next, you move down to N3, the deepest sleep stage. Then, you return to N2 before moving on to REM sleep.

So, the order goes — N1, N2, N3, N2, REM. And… repeat.

Usually, there’s a short awakening after REM sleep and before you go back into N1 sleep, but you may not remember it.

This cycle takes around 90–110 minutes, and people typically complete 4–5 cycles each night.

As the night goes on, the REM part of the cycle gets longer. You spend about 25% of your sleep time in the REM phase and 45% in N2.

Each sleep phase is associated with different kinds of activity in your brain. 

Riding your brain waves

You might have heard the term “brain waves,” but what are they? 

When you measure the activity of someone’s brain using an electroencephalogram (EEG), it appears on the screen as a wave, hence the name. But what’s making these waves? 

As you can imagine, a lot of information is getting passed around your brain. And brain cells called neurons carry these messages.

Neurons don’t just send information from A to B, they also communicate with their neighbors. When big groups of neurons synchronize, they oscillate in unison, giving rise to the brain waves we see on an EEG. 

There are many mysteries left to solve about these oscillations, but that’s beyond the scope of this article. 

The important thing for us here is that brain waves change during sleep, and these changes help experts determine which sleep phase someone is in.

Awake but sleepy

When you’re drowsy or relaxed and have your eyes closed, alpha waves are dominant. These waves have a frequency of 8–13 cycles per second, or hertz (Hz).

Alpha waves are mostly generated in your occipital lobe — the bit of your brain that deals with vision. They tend to start up in the hazy boundary between being alert and asleep.

N1: Start your descent

During N1 sleep — the lightest sleep phase — awareness of your surroundings floats away. Theta brain waves take over, which are slower than alpha waves at around 4–8 Hz. 

This steady rhythm is mostly generated by the hippocampus, a bit of your brain that’s important in memory. Scientists think that these slow waves help us solidify memories during the night.

N2: Getting deeper

As you drift deeper into N2 sleep, we meet mysterious-sounding sleep spindles and K-complexes.

Sleep spindles are “brief, powerful bursts of neuronal firing.” And K-complexes are long delta waves (more on them shortly) that last for around 1 second.

Experts believe that both of these features also help consolidate or stabilize memories while you sleep. 

In this phase, your breathing slows, as does your heart rate, and your blood pressure drops. By now, you have virtually no conscious awareness of what’s happening around you.

N3: The depths

Diving deeper into sleep, you hit the N3 stage. Here, we see delta waves, which clock in at 0.5–4 Hz. These are even lower frequency — sometimes, there’s just one oscillation every couple of seconds. 

These relatively sluggish delta waves give rise to an alternative name for non-REM sleep — slow-wave sleep.

Although slow, these waves have a high amplitude, so while the line on the EEG monitor moves up and down slowly, the peaks and troughs are pronounced.

At this point in your sleep cycle, you’re very difficult to wake. Even sounds of up to 100 decibels — roughly the volume of a jackhammer — might not rouse you.

If you do wake up during N3, you’ll likely feel very groggy and confused, which is called sleep inertia. 

That’s why experts advise that a nap should be less than 30 minutes or around 90 minutes — anything else and you might be in N3 sleep.

REM: Dream time

Finally, you enter the palace of dreams — REM sleep, where most of your dreaming takes place.

We should mention that dreams can also appear in N1 and N2, but they feel less dreamlike and more like daydreaming.

Here in REM sleep, you’ll have beta and gamma waves that are very similar to the brain waves you have when you're awake.

They measure 20–80 Hz, and, when you’re awake, they’re associated with focusing on a task, especially ones that involve very careful movements.

During REM sleep, as the name suggests, your eyes move about beneath your closed eyelids. Also, your breathing becomes more erratic, and your heart rate and blood pressure rise to levels similar to when you’re awake.

Although your brain is busy, it can be difficult to rouse someone during REM sleep. 

Taking out the trash

As you go about your daily business, metabolic bits and bobs can build up in between the cells of your brain. This can include unwanted proteins, excess fluid, and the products of metabolic processes.

Neurons are particularly sensitive to their environment, so this daily buildup of garbage would be a serious problem if it were left hanging around.

Luckily, there’s no need to worry: The recently discovered glymphatic system does the cleanup work for you. And this rubbish-removal system almost exclusively works while you’re asleep.

During non-REM sleep, gaps between the cells in your brain expand, allowing fluid to move between them, flushing the crud away.

Sleep: Bits of your brain

Next, let’s look at some of the brain regions involved in sleep. 


The hypothalamus is a small, pea-sized structure near the center of your brain. It’s a major link between your nervous system and your hormonal system. 

One of its main jobs is maintaining homeostasis — keeping your internal world stable. 

It “listens” to signals from inside and outside your body and ensures your blood pressure, heart rate, and body temperature are aligned with what’s going on.

For instance, if your body gets too hot, your hypothalamus is alerted and releases hormones that get your body to start sweating. And if you start running, it’ll increase your blood pressure and heart rate.

As you’re getting ready to sleep, the hypothalamus dampens down activity in “arousal centers” in your brain. This helps you drift off and stay asleep.

Some of the neurotransmitters released by the hypothalamus are called orexins. They help control a wide range of functions, from feeding to sleep. 

A lack of nerves that produce orexins is responsible for narcolepsy — a condition characterized by overwhelming daytime drowsiness and sudden attacks of sleep. 

Also, within the hypothalamus, there’s a tiny region called the suprachiasmatic nucleus (SCN).

The SCN is in charge of circadian rhythms, including your daily sleep-wake cycle. This region responds to the light-dark cycle and regulates melatonin production.

The mystical pineal gland

Your pineal gland is shaped a little like the nuts inside a pine cone, hence the name.

Historically, people have considered the pineal to be somewhat mystical, perhaps partly because it sits right in the center of your brain.

For instance, the 17th century scientist-philosopher René Descartes described the pineal gland as the “seat of the soul.” 

Others have called it the “third eye.” This nickname holds slightly more water because messages running from your SCN to the pineal gland provide information about the light-dark cycle. 

These communications spur the pineal gland to release melatonin as bedtime approaches. And melatonin promotes feelings of sleepiness, helping you drift off.

Brain stem lockdown

Your brain stem connects your spinal cord to the base of your brain. It plays an important part in a lot of mission-critical tasks, including breathing.

The brain stem communicates with the nearby hypothalamus. Both produce a neurotransmitter called GABA, which inhibits, or damps down, activity in your brain’s arousal centers.

Importantly, while you’re dreaming, the brainstem keeps muscles involved in movement paralyzed. 

This ensures you don’t jump out of bed or thrash around when you dream about being chased by a six-legged turquoise kangaroo, for instance.

The thalamus: A sensory gateway

When you see, touch, or hear something, sensory information is first sent to your thalamus — a small, egg-shaped structure deep inside your brain. From there, the information is shipped out to relevant parts of the brain for processing.

When you’re asleep, this sensory relay station stops relaying messages — unless it’s a potentially life-threatening situation. 

That’s why, during non-REM sleep, you don’t respond to sounds and other external events — the messages make it to the thalamus, but they don’t get forwarded on to the bits of the brain that make you aware of them.

However, when you enter the dream-filled realm of REM sleep, the thalamus gets busy again.

But rather than sending sensory signals from the outside world to the rest of your brain, it relays information from a part of the brainstem called the pons.

The pons may play a role in generating your dreams.

The emotional amygdala

Your amygdala — another deep region of your brain — is important for processing emotions, among other things. 

During REM sleep, these two almond-shaped bundles of neurons become highly active.

Experts believe this activity helps us process and store emotional memories and explains why some dreams can really give you the feels. 

Activity in the amygdala might be why sleeping on a problem is a good idea — when you wake up, things often seem less terrible. 

It also helps explain why a good night’s sleep might make you feel more emotionally stable. And why after a poor night’s sleep, you might be more prone to anxiety.

Give your brain a rest

We’ll leave it there, but as you can imagine, we could go on. There’s so much to discover about the brain and sleep. 

Although there’s still a lot that scientists don’t understand, over the last few decades, researchers have built up a pretty good picture of some of the main actors.

So, next time you’re curling up in bed, ready for some shut-eye, take a moment to consider the incredible performance that’s about to go on between your ears.


Alpha wave. (2020). 

Anatomy and function of the hypothalamus. (2018). 

Beta wave. (2009). 

Brain basics: Understanding sleep. (2022). 

Brain waves. (n.d.). 

Deep sleep maintains learning efficiency of the human brain. Nature Communications. (2017). 

Human amygdala activation during rapid eye movements of rapid eye movement sleep: an intracranial study. Journal of Sleep Research. (2016). 

Hypothalamic control of sleep. Sleep Medicine. (2007). 

Hypothalamic regulation of sleep and arousal. Annals of the New York Academy of Sciences. (2008). 

Narcolepsy. (2017). 

Noise sources and their effects. 2000). 

Orexins, sleep, and blood pressure. Sleep and Hypertension. (2018). 

Overanxious and underslept. Nature Human Behavior. (2019). 

Physiology of the pineal gland and melatonin. (2019). 

Physiology, sleep stages. (2022). 

Pineal gland as the source of the soul and third eye. Practical Neurology. (2022). 

Regional cerebral blood flow throughout the sleep-wake cycle. An H2(15)O PET study. Brain. (1997). 

REM sleep depotentiates amygdala activity to previous emotional experiences. Current Biology. (2021). 

Sleep drives metabolite clearance from the adult brain. Science. (2014). 

The glymphatic system – a beginner's guide. Neurochemical Research. (2015).