Why am I waking up at 3am? - Root Functional Medicine

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:

causes of insomnia

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.

At Root, we check 4 point cortisol curves in order to assess HPA axis function.

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.

leaky gut


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.


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 – check out our shop page for 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.


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.

insulin resistance

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.

hormone balance


Insomnia treatment, just like hormone balance, requires a whole-body approach. Do you need someone to dig for root causes, connect the dots, and create a personalized wellness plan to reverse insomnia? Check out our Get to the Root plans.


Functional medicine for business

Are sleep difficulties and daytime fatigue affecting your employees’ productivity? Check out our functional medicine for business plans where we include a 4-point cortisol curve to get an accurate physiologic picture of how the body is functioning, with actionable lifestyle changes to improve energy, focus, and productivity now.

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