causes of insomnia

Why am I waking up at 3am?

Have you ever woken up at 3 am, heart pounding, sweating and suddenly wide awake? Only to continue to lie awake wondering if and when you might fall back asleep, and wondering what caused you to wake so suddenly.

Insomnia (including trouble falling asleep, waking up throughout the night, or early morning awakening) is a symptom of an underlying imbalance.

Instead of relying on sleep aid medications (which were found to be metabolized slower in women after being on the market!), we have a different approach to resolving insomnia at the root cause. Each person’s reason for insomnia may be different – 10 different people might have ten different reasons that they wake up at 3am.  Finding and treating those root causes requires a whole body, personalized approach.

Here are some possible root causes of waking up at 3am:
image of bed with text over image root causes of insomnia -Blood Sugar Imbalance -Hormone Imbalance -Cortisol -HPA Axis Dysfunction -Melatonin Production -Dysbiosis and Inflammation -Sleep Apnea -Environmental Toxins -Leaky Gut -Nutrient Deficiency

HPA axis dysfunction 

HPA axis stands for hypothalamic, pituitary, and adrenal axis. Your adrenal glands secrete cortisol in response to signals from your brain (hypothalamus and pituitary). In an idealistic situation we want to see your cortisol levels higher in the am (to get you up and ready for the day!) and lower at night so that you can fall asleep. If your cortisol is high before bed, you’ll have trouble falling asleep. If your cortisol does not stay low overnight, or if cortisol starts spiking early, you’ll likely have middle of the night awakening. The brain is very perceptive and it also likes patterns so if you’re subconsciously preparing for the next days’ stress (or if you had been exposed to stressful situations in the recent past), this will lead to HPA axis dysfunction and insomnia.

Melatonin imbalance 

The next thing about cortisol is that cortisol and melatonin work oppositely of each other. Cortisol suppresses melatonin during the day and then melatonin suppresses cortisol  levels in the evening and at night. But, if cortisol stays high before bed, your body won’t be functionally optimizing melatonin.

What else suppresses melatonin:
There’s light in your room at night. The best sleeping environment is a near pitch black room. This includes exposure to blue light from devices 1-2 hours before bed.
You’re not getting enough light during day. While blue light from devices may have the most pronounced suppressant effect on melatonin, recent studies show that full spectrum light throughout the day can counterbalance blue light exposure. As we head into fall and winter months, using a light box for 30-60 minutes in the morning can help to reset melatonin cycles.

Sleep Apnea

Sleep apnea is the most prevalent sleep disorder. Sleep apnea is also a common comorbidity of Hashimoto’s thyroid disease. Studies have found that 25-35% of people with hypothyroidism also have sleep apnea and that sleep apnea is a risk factor for Hashimoto’s.

Leaky gut 

Leaky gut is a common root cause of inflammation. Just under the lining of the intestinal cells is the vast majority of the body’s immune system. When this gets activated, the inflammation does not just stay in the gut, it circulates throughout causing cortisol imbalances, and systemic symptoms. Newer studies show that anxiety, depression, and insomnia are actually disorders of inflammation.

Our favorite Gut Health Rebalance supplement can be taken as a powder in water, or added to your morning smoothie.

Gut Health Rebalance

Gut Health Rebalance

The perfect synergy of ingredients to soothe and improve the gut lining FAST.


The gut-brain axis is complicated and we’ll plan on doing more posts on this in the future. Leaky gut can be both a cause of anxiety and a result of cortisol imbalance from stress. Anxiety most commonly occurs at night. When our minds are not occupied, they wander. Even when it seems impossible to be experiencing anxiety in the middle of the night when you are sound asleep, remember that 1: anxiety is often an underlying inflammatory issue and 2. Your brain likes patterns and will trigger the release of cortisol even when it might not be warranted for the situation if HPA axis dysfunction is present.  If you have trouble calming your mind at night due to anxiety, we often suggest Root Sleep Support because it contains a calming blend of herbs and minerals to promote relaxation and restful sleep.  

Environmental triggers 

This is not an exhaustive list, but we’ll start with the most common ones:
Alcohol. Alcohol notoriously causes rebound anxiety and 3am awakenings for many people. Even though it might seem like a glass or two of wine helps with falling asleep, the quality of sleep is affected by alcohol, leading to middle of the night and early morning awakening.
Caffeine. The half-life of caffeine is 6-8 hours. That means if you drink coffee at 1pm, half of that caffeine may still present at 9pm, making it harder for you to relax before bed. Also, you may have a genetic SNP that makes it harder to metabolize caffeine. This SNP is part of what we can test for at Root – Here is a very comprehensive nutrition genome report!

Nutrient Deficiency

Are you lacking nutrients like the essential amino acid tryptophan, which is used to make serotonin and melatonin? We can test for this in our functional labs, as well as your gut health to be sure you are breaking down and absorbing proteins.
Magnesium deficiency is a common deficiency. Magnesium powers detox reactions (occurring mostly at night!), relaxes muscles, and helps anxiety. We wrote more about magnesium here. Our favorite highly absorbable magnesium supplement can be found here.

sleep support

Sleep Support

A calming blend of minerals and herbs that promote muscle relaxation and more restful sleep.
Magnesium glycinate

Magnesium Glycinate

The calming mineral we may need more of in our life…
magnesium combo

Magnesium Combo

Three forms of highly absorbable magnesium in one capsule.

Blood sugar imbalance

Having an unbalanced plate without fiber, protein, and healthy fat can lead to a cycle of blood sugar spikes, then insulin spikes, then blood sugar drops. When blood sugar drops, your body’s protective mechanism is to secrete cortisol to bring your blood sugar back up.
Insulin resistance can also lead to after dinner food cravings and later evening snacking.  Eating at night raises body temperature, which makes it harder to fall asleep.

Hormone imbalance

Estrogen/serotonin/melatonin are all related. Estrogen works throughout the body, including the brain. In the brain, estrogen can regulate serotonin. Serotonin is used by the body to make melatonin. Balancing hormones at Root is a multi-layered approach.

To balance hormones, we balance blood sugar by eating protein/fat/fiber at each meal, supplement important nutrients, and manage stress and sleep with some of the tips in this article. 

sleep support

Sleep Support

A calming blend of minerals and herbs that promote muscle relaxation and more restful sleep.
Magnesium glycinate

Magnesium Glycinate

The calming mineral we may need more of in our life…

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