Why Am I Waking Up In The Middle Of The Night?

Updated: Jan 13, 2020

Are you one of many people who wake up between 2 and 4 am? After you wake up, It may take some time for you to fall back to sleep. The quality of your sleep is poor, and you don’t feel refreshed and restored when you wake up. You may even be getting sick more often as a result. What’s going on?

Sleep disturbances are an often ignored yet common problem that can lead to more health issues. In this article, we’ll discuss the reasons why you’re waking up and what you can do about it.

Fatty Liver Disease and Your Circadian Rhythm

Usually, the most common cause of waking up between 1-4: 00 am is a liver problem.

It may be that you have liver inflammation or fatty liver disease, also known as non-alcoholic fatty liver disease. Fatty liver disease is a condition where fat builds up in your liver because of a poor diet, blood sugar problems, or accumulated toxins.

It is estimated that fatty liver disease affects 20-30% of the population in Western countries. Often, there are no clear symptoms of fatty liver disease.

When your liver becomes burdened by accumulated fat, it can no longer efficiently and effectively cleanse and detoxify your body. Since toxins cannot be safely neutralized and removed from the body, the risk of degenerative diseases increases. Fatty liver disease almost always coincides with insulin resistance and the development of type 2 diabetes.

What does the liver have to do with waking up between 1-4am?

Our circadian rhythm is our master ‘internal clock’ and ensures that all of our organs and internal biological systems work harmoniously together. It is during the period between 1 and 3 AM that the liver works it’s hardest to cleanse and detoxify our body while we sleep.

So if your liver is slow and stagnant from an accumulation of fat during the liver cleansing time (1-4am), the body will try to allocate more energy for detoxification and trigger your nervous system to wake you up.

How do I know if I have fatty liver disease?

Your doctor can order blood tests or can conduct an ultrasound to test for this condition. If your liver enzymes and other liver biomarkers come back normal, you still may have a fatty liver - an ultrasound is the most sensitive test for evaluation.

What are the consequences of fatty liver disease?

If you have fatty liver disease your chances of developing type 2 diabetes and heart disease dramatically increases. Your sleep can be impacted, and your energy levels can drop.

It’s common for patients with fatty liver disease to have persistent fatigue. Also, when a person has fatty liver disease, it can be challenging to lose weight. The liver must be healthy to effectively burn stored fat.

What Can You Do?

A functional medicine evaluation would be very beneficial. Not only would the confirmatory tests be ordered but additional testing would be done to assess underlying biochemical imbalances. Addressing underlying conditions before they cause more significant symptoms is crucial.

A functional medicine doctor does not only address a liver problem but can help support the healthy function of your entire body. That means if you have an underlying bacterial infection in your intestines that is causing your liver to be overwhelmed, addressing that infection will speed up liver healing.

You can also help your body restore optimal liver function by overhauling your diet. A diet that is high in refined grains, high-fat animal protein, conventional (not organic) produce and refined sugars will burden your liver with too many toxins and too much fat.

A diet rich in fruits, vegetables, nuts, seeds, lean proteins and healthy fats will provide your liver (and the rest of your body) with much needed nutritional support for optimal function.

Other Causes of Sleep Disturbance

Sleep Apnea

Ruling out sleep apnea is important. Ask your partner if you snore, if you do, there’s an excellent chance you have sleep apnea. How loud someone snores is often seen as only a nuisance, but it could potentially be a sign of a serious problem.

Sleep apnea independently increases your risk of dying from heart disease and developing type 2 diabetes. Sleep apnea is also correlated strongly with obesity.


With nocturnal hypoglycemia, your blood sugar drops so suddenly and significantly that your body wakes you up to raise your blood sugar.

Nocturnal hypoglycemia can be caused by a poor diet filled with processed food or a diet with very low carbohydrates which causes your body and brain are starving for adequate blood sugar.

When you are asleep your body needs fuel for its regenerative processes. If you have eaten a balanced diet during the day and have no issues with insulin resistance, then your body will usually have no diet-related sleep problems.

I have seen it both ways - patients who are eating a diet filled with processed junk and others who are on a strict low carbohydrate diet - and both have sleep problems.

Be sure you are eating balanced meals throughout the day - protein, healthy fat, and some form of carbohydrates. Eat plenty of fruits and vegetables and cut out refined sugar.

Viral Infections

A persistent and chronic viral infection may be the culprit of your sleep disturbances. If you’ve had a mononucleosis infection (mono) in the past or a shingles outbreak or have herpes or another significant infection, then there may be a viral component to your sleep problems.

Viruses can lay dormant for years and then reactivate and grow stronger if your immune system is compromised by chronic stress, a poor diet, toxin build-up, or emotional or physical trauma.

A chronic viral infection can attack your nerves and cause the nerves predominantly used during sleep to become sensitive and irritated making restful sleep difficult.


Thinking about all of your problems or things you have to do tomorrow before you go to bed can keep your nervous system in ‘panic mode’ and make deep sleep difficult. There is often a stress component to each of the above factors.

No matter which factor is causing you to wake up during the night, it will be important to address your stress levels.

Shut off your phone, computer, and TV at least an hour before bed. Engage in low-key, relaxing activities to acclimate your body to sleep. Make sure that you use your blue light reducing settings on your phone and computer so that when the sun goes down, your circadian rhythm does not get confused by your devices.

Dark or 'blackout' curtains for your bedroom will help ensure that light is not what is keeping you up at night.

The Importance of Treating the Whole Person

Waking up in the middle of the night is common. The most common cause is a liver problem, but there may be other reasons why your sleep is disrupted including sleep apnea, nocturnal hypoglycemia, viral infection, urinary issues, digestive issues, potential food allergies or stress.

Remember that the information in this article does not replace the advice or treatment from your doctor. The incorporation of relevant testing, genetic data, symptoms, nutrient deficiencies and health condition of the individual is needed to fully asses what is going on when a person has frequent sleep disturbance.

The key is to identify the cause and address the imbalances. If the cause of your imbalances is treated then not only will your sleep improve, your overall health will as well.

Read more about how Functional Medicine and our article 'Benefits of a Circadian Rhythm Reset'

If you would like to speak to me to ask questions about functional medicine, sleep or how I can help you, please schedule a Free 15 Minute Consultation or call or text my office at 913-728-5291.


#Sleep #ViralInfection #SleepApnea #Infection #Insomnia #Hypoglycemia #Fattyliver #NAFLD


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