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Blog/Sleep/7 min read

Waking Up at 3am: 5 Root Causes and How to Test Them

By Martha Lewis, FDN-P | Functional Sleep Detective9/16/2026
Waking Up at 3am: 5 Root Causes and How to Test Them

About Martha


Key Takeaways

  • The five most common reasons Martha sees for 3am waking are cortisol, blood sugar, gut health, toxins and liver detox, and neurotransmitters — and most of her clients have a combination of several, not just one.
  • Blood sugar crashes, gut pathogens that are most active at night, and toxins the liver can't clear all create stress or inflammation, which triggers a cortisol release in the middle of the night that wakes you up feeling wired.
  • Martha uses the Hormone Zoomer, which measures cortisol from five samples across the day, alongside gut, neurotransmitter, and toxin testing — because a single blood draw only shows cortisol at one moment in time.


If you fall asleep fine but wake up at 3am wide awake, your brain alert and racing, sleep hygiene isn't the fix. This was my main problem. I stopped watching TV before bed and stopped eating chocolate in the evening — and still woke up in the middle of the night.


My sleep went from great to not in late pregnancy, and it didn't go away after I had my son. It took me two years to realize that not sleeping normally is a symptom that something else is going on in the body.


By the time you have that symptom, more than one system is affected. So while I'm going to walk through five causes, most of my clients have a combination of them.


1. Cortisol that's high in the middle of the night


The most common thing I see in clients who wake at 3am is cortisol that's really high in the middle of the night. Cortisol raises blood sugar, puts glucose into the cells, and keeps you alert during the day — which is exactly why it should be at its lowest at night.


If you wake up wired, like your brain does not want to be asleep, your body is probably releasing cortisol. When the body has been stressed for a long time, cortisol can become depleted and it resorts to adrenaline instead, which makes you even more wired and anxious.


A supplement to lower cortisol doesn't get to the root of what's causing it. The body releases cortisol when it's stressed or when there's inflammation. So the real question is what's creating that stress and inflammation at 3am.


2. Blood sugar dropping too low


When blood sugar drops too low, the body releases cortisol to raise it. If your blood sugar is on an extreme roller coaster of spikes and drops during the day, that roller coaster continues into the night.


The signs I look for include needing to eat every two to three hours, getting hangry if you go too long without eating, and getting a lot of energy after eating. I see this in many clients who eat very well, exercise, and care about their health.


Most labs call fasting glucose up to 100 normal. I like to see it between 75 and 90.


But bloodwork only shows that one second in time, so I recommend many of my clients get a continuous glucose monitor. I use one called Lingo — it's $89 for two sensors, and you don't need a prescription [Lingo link + 15% discount code — Martha to provide]. You don't need any testing to start working on this now.


3. Gut pathogens that are most active at night


Parasites, H. pylori (a bacteria that lives in the stomach), and candida (a type of yeast) are all most active in the middle of the night. That's when they're eating, excreting, and releasing toxins that cause inflammation. The body releases cortisol as an anti-inflammatory hormone to deal with it — and that wakes you up.


I had a parasite I think I got from traveling to Nepal and India 13 years before. My body stayed in balance for a long time, but having a baby at age 39 was just too much stress.


When I tested my cortisol with the Hormone Zoomer, which takes samples five times throughout the day, my cortisol was higher in the middle of the night than at any other point in the day. It's supposed to be the opposite.


Leaky gut adds to this, letting undigested food and toxins leak into the bloodstream and cause more inflammation.


4. Toxins and an overloaded liver


The liver is also most active in the middle of the night. When there are more toxins than it can get rid of, they circulate and cause inflammation, which makes the body release cortisol.


The hormone test I run shows how estrogen, progesterone, and testosterone are being broken down. If estrogen is building up, the liver isn't getting rid of it like it should.


I also test directly for mycotoxins from mold, environmental chemicals like pesticides, heavy metals, and PFAs — the forever chemicals.


5. Depleted neurotransmitters


Neurotransmitters don't necessarily cause high cortisol at night, but they definitely affect sleep. Good gut bacteria are responsible for making up to 90% of the neurotransmitters in the gut, and when pathogens take over, those good bacteria get depleted.


My serotonin, dopamine, and GABA were all depleted. Many of my clients are very depleted in these calming, sleep-supporting neurotransmitters.


Why you have to test for everything at once


Everything affects everything else. When the body is constantly stressed and making cortisol, it doesn't prioritize estrogen, progesterone, and testosterone, so those become depleted too.


If we only deal with a parasite but don't look at blood sugar, neurotransmitters, and toxins, you're probably not going to get better. That's why I test for everything from the beginning.


Conventional doctors aren't ordering these tests, and insurance doesn't cover them because they aren't diagnostic. My bloodwork was always perfect — but I had a parasite, depleted hormones and neurotransmitters, and heavy metals.


You don't have to wait for lab results to start. At least half of my clients start getting an hour more of sleep a night just from working on the things in their jump start plan while their labs are processing.


FAQ

Q: Why do I wake up at 3am every night?

A: The most common reason is cortisol that's high in the middle of the night, when it should be at its lowest. The body releases cortisol when it's stressed or inflamed, and at 3am that's usually driven by blood sugar dropping, gut pathogens, or toxins the liver can't clear. That's why you wake up feeling wired and alert instead of groggy.


Q: Can low blood sugar wake you up at night?

A: Yes. When blood sugar drops too low, the body releases cortisol to raise it, and that cortisol wakes you up. If you need to eat every two to three hours or get hangry when you go too long without food, a continuous glucose monitor will show you what your blood sugar is doing overnight.


Q: Can I just take a supplement to lower my cortisol?

A: You can, but it won't get to the root of why your body is releasing cortisol at night. Cortisol is a response to stress or inflammation, so the fix is finding what's causing it — blood sugar swings, gut pathogens, toxins, or a combination of all three.


Q: Why does my bloodwork look normal if I can't sleep?

A: Standard bloodwork only captures one moment in time, so it can't show your cortisol rising at 3am or your blood sugar dropping overnight. Conventional doctors also don't order functional tests like the Hormone Zoomer, and insurance doesn't cover them because they aren't diagnostic. Martha's own bloodwork was always perfect while she had a parasite, depleted hormones and neurotransmitters, and heavy metals.


If cortisol, blood sugar, gut pathogens, toxins, or neurotransmitters might be affecting your sleep, this is exactly what the Complete Sleep Solution program investigates. The program includes four functional lab panels — covering hormones and cortisol, gut health, neurotransmitters, and toxins — that identify every root cause at once so you know exactly what's keeping you awake.


→ Learn how the Complete Sleep Solution program works 


About Martha Lewis 

Martha Lewis is a certified Functional Diagnostic Nutrition practitioner and founder of The Sleep Detective™. Since 2019, she has helped 300+ clients identify the root causes of their insomnia using functional lab testing — including gut analysis, hormone panels, neurotransmitter testing, and toxin screening. She discovered her own root causes (hormone imbalances, heavy metals, and a parasite) after years of trying conventional sleep solutions, and now uses the same investigative approach with her clients.


Learn more about Martha →

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