Root Causes of Insomnia: 6 Overlooked Reasons You Can’t Fall Asleep or Stay Asleep

Insomnia is one of the most frustrating sleep problems a person can experience. You may have trouble falling asleep, wake up throughout the night, or find yourself wide awake at 2, 3, or 4 AM with your mind racing. The next day, poor sleep often shows up as fatigue, brain fog, irritability, poor concentration, sugar cravings, low motivation, and the need for more caffeine just to function.

But here is the important point: insomnia is often not the real root problem. Insomnia is usually a symptom that something deeper in the body is out of balance.

If you have thyroid disease, Hashimoto’s disease, Graves’ disease, chronic inflammation, autoimmune disease, blood sugar problems, hormone imbalance, anxiety, or adrenal stress, then trouble falling asleep or trouble staying asleep may be connected to more than just poor sleep habits.

In functional medicine, I look at insomnia differently. Instead of asking only what you can take to force sleep, I want to understand why your body will not allow you to sleep normally in the first place.

For some people, the root cause of insomnia is high cortisol at night. For others, it may be blood sugar instability, chronic pain, inflammation, estrogen dominance, progesterone imbalance, COMT gene variations, or a glutamate and GABA imbalance.

In this article, I’ll walk you through six overlooked root causes of insomnia and explain why sleep problems often require a deeper look than melatonin, sleep medications, or basic sleep hygiene.

What Is Insomnia?

Insomnia is a common sleep disorder that can make it difficult to fall asleep, stay asleep, or wake up feeling rested. Some people with insomnia lie awake for hours before finally falling asleep. Others fall asleep easily but wake up in the middle of the night and cannot get back to sleep.

There are several common insomnia patterns:

• Trouble falling asleep
• Trouble staying asleep
• Waking up between 2 AM and 4 AM
• Waking too early in the morning
• Sleeping through the night but waking up exhausted
• Feeling tired all day but wired at night

These patterns matter because they can point to different underlying causes. The person who cannot fall asleep may have a different root cause than the person who wakes up at 3 AM every night.

This is why treating all insomnia the same way often fails.

Why Poor Sleep Becomes a Vicious Cycle

Poor sleep can quickly become a vicious cycle.

You can’t sleep at night, so you wake up tired. Because you are tired, you reach for coffee, soda, energy drinks, sugar, or carbohydrates to push through the day. That may temporarily help your energy, but it can also worsen blood sugar swings, cortisol rhythm, anxiety, and nighttime alertness.

Then bedtime comes, and instead of feeling calm and sleepy, your body feels restless. Your mind races. Your legs twitch. You toss and turn. You may feel exhausted, but your brain will not shut off.

Then you wake up tired again, and the cycle repeats.

This is why insomnia should not be viewed only as a nighttime problem. Many of the root causes of insomnia occur during the day through blood sugar instability, stress hormones, inflammation, caffeine use, hormone imbalance, and nervous system dysregulation.

6 Overlooked Root Causes of Insomnia

When I work with patients who struggle with chronic insomnia, I want to know what kind of sleep problem they have and what other symptoms are happening alongside it.

Do they also have thyroid problems? Blood sugar issues? Autoimmune disease? Pain? Anxiety? Hormonal symptoms? Brain fog? Fatigue? Restless legs? Nighttime heart racing? Digestive problems?

These clues help us look at the bigger picture.

Here are six overlooked root causes of insomnia that I often evaluate in patients who have trouble falling asleep, trouble staying asleep, or waking up in the middle of the night.

1. High Cortisol at Night and Low Melatonin

One of the most common patterns I see in people with fatigue and insomnia is high nighttime cortisol.

Cortisol is a hormone made by the adrenal glands, which sit on top of your kidneys. Cortisol is involved in energy, blood sugar regulation, inflammation, immune function, thyroid function, hormone balance, and the body’s fight-or-flight response.

Cortisol should follow a daily rhythm. It should be higher in the morning to help you wake up and feel alert. It should gradually decline throughout the day and be lower at night so melatonin can rise and help you sleep.

When cortisol stays high at night, you may feel tired but wired. Your body is exhausted, but your brain is alert. You may feel restless, anxious, overstimulated, or unable to settle down.

Research studies show that cortisol and the stress system can play an important role in chronic insomnia. When cortisol is high at night, melatonin may be lower. Since melatonin helps signal sleep, low melatonin can make it harder to feel sleepy at the right time.

This is one reason melatonin does not work for everyone. The problem may not be that you simply need more melatonin. The bigger issue may be that cortisol is too high at the wrong time of day.

Symptoms of High Nighttime Cortisol

High nighttime cortisol may cause symptoms such as:

• Feeling tired but wired at night
• Racing thoughts when trying to sleep
• Trouble falling asleep
• Waking up with a second wind
• Restlessness in the evening
• Anxiety at bedtime
• Light sleep or frequent waking
• Feeling exhausted in the morning

If this sounds like you, then the root cause of your insomnia may involve your adrenal glands, cortisol rhythm, blood sugar, inflammation, or chronic stress physiology.

Why Saliva Cortisol Testing Can Be Helpful

The best way to understand cortisol rhythm and high cortisol in the evening is through testing.

Cortisol can be tested in blood or saliva, but when insomnia is the problem, a saliva cortisol test is often more useful because it can measure cortisol at several points throughout the day.

A single morning blood cortisol test may look normal, but it can completely miss high evening cortisol or abnormal nighttime cortisol patterns.

A saliva cortisol test can measure cortisol in the morning, afternoon, evening, and before bed. This gives a more complete picture of whether cortisol is rising when it should be falling.

If you have trouble falling asleep because you feel wired at night, testing cortisol rhythm can be an important step.

Read: The Connection Between High Cortisol and Sleep Disturbances

2. Blood Sugar Imbalances and Waking Up at 2, 3, or 4 AM

Another overlooked root cause of insomnia is blood sugar instability.

This is especially important for people who fall asleep easily but wake up between 2 AM and 4 AM. If this is your pattern, your sleep problem may be connected to nighttime blood sugar drops.

Your body does not like low blood sugar. If glucose drops too low during the night, your adrenal glands may release cortisol and adrenaline “stress hormones” to help bring blood sugar back up. Those hormones can wake up your brain and body.

You may wake suddenly with your mind racing, your heart pounding, or a sense of restlessness. Some people feel hungry, anxious, hot, shaky, or wide awake.

This is why blood sugar and insomnia are so connected.

People with diabetes, insulin resistance, hypoglycemia, reactive hypoglycemia, thyroid disease, or chronic stress may be more likely to experience sleep problems related to blood sugar swings.

Blood Sugar, Thyroid Disease, and Insomnia

Blood sugar problems and thyroid problems often overlap. I have talked more about the blood sugar and thyroid connection because this is such an important pattern in people with Hashimoto’s, hypothyroidism, fatigue, weight gain, and insomnia.

If you wake up at 2, 3, or 4 AM, especially if you also have sugar cravings, caffeine dependence, afternoon crashes, irritability when skipping meals, or belly fat, blood sugar may be a major piece of your insomnia puzzle.

One of the new patient forms I use is a metabolic assessment form because symptoms can often point us toward blood sugar instability before it becomes obvious on basic lab work.

Signs Blood Sugar May Be Affecting Your Sleep

Blood sugar may be contributing to insomnia if you:

• Wake up between 2 AM and 4 AM
• Feel shaky, anxious, or hungry at night
• Need caffeine to function in the morning
• Crash in the afternoon
• Feel irritable when meals are delayed
• Crave sugar or carbohydrates
• Have elevated fasting glucose, A1C, insulin, or triglycerides
• Have thyroid disease, insulin resistance, or hypoglycemia

If your sleep problems are rooted in blood sugar instability, taking sleep supplements alone may not fix the problem. You have to stabilize the physiology that is waking your body up.

Read: 12 tips to balance your blood sugar when you have thyroid disease.

3. Pain, Inflammation, and Autoimmune Stress

Pain and inflammation are major causes of poor sleep and elevated stress hormones. They are often overlooked when people talk about insomnia.

If your body is chronically inflamed, your nervous system may stay activated. Inflammation can disrupt cortisol rhythm, increase pain sensitivity, affect neurotransmitters, and interfere with deep restorative sleep.

Studies show that the stress system and inflammatory signaling are closely connected in chronic insomnia and stress-related disorders. Chronic inflammation can keep the body in a heightened state of alertness, which makes it harder to fall asleep and stay asleep.

I often see insomnia in patients with inflammatory and autoimmune conditions such as:

• Hashimoto’s disease
• Graves’ disease
• Rheumatoid arthritis
• Lupus
• Fibromyalgia
• Chronic joint pain
• Chronic neck, back, or shoulder pain
• Headaches or migraines
• Crohn’s disease
• Ulcerative colitis
• Other forms of inflammatory bowel disease

These conditions can create a vicious cycle. Inflammation disrupts sleep, and poor sleep increases inflammatory stress. The more this cycle continues, the harder it can be to recover.

Read: 5 Ways To Reduce Gut Inflammation and Take Control of Your Health

Symptoms of Chronic Inflammation That May Affect Sleep

Chronic inflammation may show up as:

• Joint pain or muscle pain
• Headaches
• Brain fog
• Fatigue
• Skin problems
• Digestive symptoms
• Autoimmune flares
• Poor recovery after exercise
• Chronic stiffness
• Nighttime discomfort
• Restless sleep

If pain and inflammation are driving your insomnia, then the real solution is not just a stronger sleep aid. The root cause needs to be identified and addressed. That may include evaluating gut health, food triggers, autoimmune activity, blood sugar, hormone balance, infections, toxin exposure, stress physiology, or nutrient deficiencies.

 

4. COMT Gene Variations and Excess Fight-or-Flight Activity

Another overlooked contributor to insomnia is the COMT gene.

COMT stands for catechol-O-methyltransferase. This gene plays a role in how the body breaks down catecholamines such as dopamine, adrenaline, and noradrenaline.

These neurotransmitters and hormones are important for focus, motivation, alertness, drive, and stress response. But when they are too high at night or not cleared properly, they can keep the brain stimulated when it should be winding down.

This is why some people with insomnia describe their symptoms as:

• Racing thoughts
• Overthinking
• Feeling stuck in fight-or-flight mode
• Anxiety at night
• Poor stress tolerance
• Light sleep
• Restlessness
• Mood swings
• Pain sensitivity
• Difficulty relaxing

The COMT gene is not the only cause of insomnia, but it can be one important piece of the puzzle in people who struggle with stress sensitivity, anxiety, mood changes, pain sensitivity, and trouble shutting their brain off.

COMT, Adrenaline, Dopamine, and Sleep

Catecholamines should help you during the day. They support motivation, focus, reaction time, and energy. But at night, high catecholamine activity is not helpful.

If your body is producing too much adrenaline or dopamine, or if you are not breaking these chemicals down efficiently, your brain may stay electrically active when it should be shifting into rest mode.

This is why insomnia is not always a melatonin problem. Sometimes the deeper issue is too much excitatory chemistry.

In root cause medicine, these patterns are worth exploring, especially when insomnia overlaps with anxiety, depression, low motivation, chronic stress, pain sensitivity, or mood swings.

Watch this Video: Understanding COMT Mutations: Anxiety, Insomnia, Hormone Imbalances, and Even Cancer

5. Estrogen Dominance, Progesterone, and Hormone Imbalances

Hormone imbalance is another common root cause of insomnia, especially in women with thyroid disease, perimenopause, menopause, PMS, irregular cycles, or a history of birth control use.

When I work with women who struggle with sleep, I want to know whether they also have signs of estrogen dominance, low progesterone, thyroid dysfunction, adrenal stress, or poor hormone clearance.

Estrogen dominance does not always mean estrogen is extremely high. It means estrogen is too dominant relative to progesterone.

A woman may have estrogen dominance when:

• Estrogen is high and progesterone is low
• Estrogen is normal but progesterone is low
• Estrogen is low but progesterone is even lower
• Estrogen is elevated due to hormone replacement therapy or poor liver clearance

This matters because progesterone has a calming effect on the brain and nervous system.

Progesterone, GABA, and Sleep Quality

Progesterone interacts with GABA receptors in the brain. GABA is one of the body’s calming neurotransmitters. When GABA activity is supported, the nervous system can settle down more easily.

This is why many women notice sleep problems around hormonal transitions such as:

• The week before their period
• Perimenopause
• Menopause
• Postpartum changes
• Coming off birth control
• Starting or changing hormone replacement therapy

Progesterone has been studied for its relationship to sleep, calming brain activity, and respiratory function. When progesterone is balanced with estrogen, it may support better sleep quality, deeper sleep, and a calmer nervous system.

But this does not mean everyone should run out and take progesterone. Hormones should be tested first. Taking hormones without understanding the pattern can make symptoms worse.

Estrogen Dominance in Men Can Also Affect Sleep

Men are not off the hook when it comes to estrogen dominance and sleep problems.

For many men diagnosed with low testosterone, the problem is not always that they simply do not make enough testosterone. In some cases, testosterone is being converted into estrogen through a process involving aromatase.

This pattern is sometimes called andropause or “male menopause.”

Men with this pattern may experience:

• Low testosterone symptoms
• Increased belly fat
• Low motivation
• Poor stamina
• Mood changes
• Low libido
• Brain fog
• Sleep problems
• Higher estrogen levels
• Insulin resistance

For both men and women, hormone imbalance can affect sleep through changes in cortisol, blood sugar, brain chemistry, body temperature, mood, and nervous system regulation.

Hormone Testing to Consider When You Have Insomnia

If a hormone imbalance may be contributing to insomnia, testing is important.

At a minimum, hormone evaluation may include:

• Estrogen levels
• Progesterone levels in women
• Testosterone levels
• Free testosterone
• Sex hormone-binding globulin (SHBG)
• DHEA
• Cortisol rhythm
• Thyroid markers

For women, a more complete option may include a comprehensive hormone panel. The goal is not just to look at one hormone number, but to understand the relationship between hormones and symptoms.

6. Glutamate and GABA Imbalances

The final overlooked root cause of insomnia is an imbalance between glutamate and GABA.

GABA is one of the brain’s main calming neurotransmitters. Glutamate is one of the brain’s main excitatory neurotransmitters. You need both, but they need to be balanced.

When glutamate activity is too high or GABA activity is too low, the brain can feel overstimulated. This can lead to racing thoughts, anxiety, restlessness, sound sensitivity, poor stress tolerance, and trouble falling asleep.

This is why some people feel physically exhausted but mentally wired.

A glutamate and GABA imbalance may be more likely when insomnia overlaps with:

• Anxiety
• Brain fog
• Chronic stress
• Histamine intolerance
• Gut problems
• Inflammation
• Mold exposure
• Headaches
• Sensitivity to supplements
• Poor detoxification
• Restless legs
• Neurological symptoms

The brain does not operate separately from the rest of the body. Gut inflammation, blood sugar instability, hormone shifts, immune activation, and chronic stress can all influence neurotransmitter balance.

Why Testing Matters When You Have Chronic Insomnia

If you have struggled with insomnia for months or years, it is important to stop thinking of sleep as an isolated problem.

The diagnosis of insomnia tells you that you are not sleeping well. It does not tell you why.

That is where many people get stuck. They try melatonin, magnesium, sleep hygiene, prescription sleep medications, CBD, teas, or relaxation apps, but they never identify what is actually disrupting sleep.

In functional medicine, we want to ask better questions:

• Is cortisol high at night?
• Is blood sugar dropping at 2 or 3 AM?
• Is inflammation driving adrenal stress?
• Is thyroid dysfunction affecting metabolism and sleep?
• Is estrogen dominance or low progesterone involved?
• Is testosterone converting into estrogen?
• Is the nervous system stuck in fight-or-flight mode?
• Is there a COMT-related issue affecting catecholamine clearance?
• Is there a glutamate and GABA imbalance?

Proper testing helps identify where the body needs support and where it does not. You cannot fix what you do not understand.

Natural Support for Insomnia Depends on the Root Cause

Many people ask, “What is the best supplement for insomnia?”

The better question is, “What is causing the insomnia?”

The right natural sleep support depends on the pattern.

If high nighttime cortisol is the issue, the strategy may focus on calming cortisol and supporting the stress response. One supplement often used for this purpose is phosphatidylserine. Phosphatidylserine has been studied for its effect on stress hormone response(*).

Some people may also benefit from calming sleep support such as Botanicalm, depending on their individual needs.

If inflammation and pain are driving insomnia, support may need to focus on inflammatory balance. In these cases, I may consider products such as Salicin B or Inflamma-bLOX as part of a broader inflammatory support strategy.

If adrenal dysregulation is involved, adrenal adaptogens may be helpful for certain patterns. Adaptogens are herbs that help support the body’s stress response. Examples include ashwagandha, rehmannia, Magnolia officinalis, and Panax ginseng.

If estrogen dominance is contributing to insomnia, support may include improving liver detoxification pathways, supporting the adrenal glands, eating more leafy greens, increasing fiber, and eating more cruciferous vegetables. In some cases, targeted support such as CDG with estrodim may be considered.

The key is that supplements should match the root cause. Randomly taking sleep supplements without understanding the pattern often leads to inconsistent results.

Lifestyle Tips That Support Better Sleep

While deeper testing may be needed for chronic insomnia, there are several foundational habits that can support better sleep.

Keep Blood Sugar Stable During the Day

Avoid skipping meals if you know you are prone to blood sugar crashes. Eat enough protein, include healthy fats, and avoid relying on sugar and caffeine to push through fatigue.

Reduce Caffeine Later in the Day

Caffeine can worsen insomnia, especially in people with high cortisol, anxiety, COMT issues, or poor detoxification. If sleep is a problem, caffeine should be evaluated carefully.

Support Your Circadian Rhythm

Morning sunlight, consistent wake times, and dimmer light in the evening can help reinforce your sleep-wake rhythm.

Avoid Intense Exercise Late at Night

Exercise is beneficial, but intense workouts late in the evening can raise cortisol and adrenaline in some people.

Address Pain and Inflammation

If pain wakes you up or prevents deep sleep, the inflammatory drivers need to be addressed. This may include gut health, food triggers, autoimmune activity, blood sugar, and stress physiology.

Test Instead of Guessing

If insomnia has been going on for months or years, guessing is usually not enough. Testing can help identify whether the problem is cortisol, blood sugar, hormones, thyroid, inflammation, or neurotransmitter-related.

Key Takeaways About the Root Causes of Insomnia

Insomnia is common, but it is not always caused by the same problem.

Some people have trouble falling asleep because cortisol is too high at night. Others wake up at 2 or 3 AM because their blood sugar drops during the night. Some people cannot sleep because pain and inflammation keep the nervous system activated. Others struggle because of hormone imbalance, COMT gene variations, or glutamate and GABA imbalance.

The most important thing to remember is that insomnia is a symptom. It is a clue that something deeper needs to be evaluated.

If you have thyroid disease, Hashimoto’s, Graves’ disease, autoimmune disease, chronic inflammation, anxiety, hormone imbalance, blood sugar problems, or adrenal stress, your sleep issues may be connected to those deeper patterns.

Once the root cause is identified, sleep often begins to improve because the body is no longer fighting against itself.

Frequently Asked Questions About Insomnia

Why do I wake up at 2 or 3 AM every night?

Waking up between 2 and 4 AM can be related to blood sugar instability, cortisol release, stress hormones, liver activity, hormone imbalance, or inflammation. One common pattern is a nighttime drop in blood sugar that triggers cortisol and adrenaline, waking the brain and body.

Can high cortisol cause insomnia?

Yes. Cortisol should be lower at night. When cortisol stays elevated in the evening, you may feel tired but wired, restless, anxious, or unable to shut your mind off.

Why does melatonin not work for me?

Melatonin may not work if your insomnia is being driven by high nighttime cortisol, blood sugar swings, inflammation, pain, hormone imbalance, or nervous system overactivation. In those cases, melatonin may not address the real reason you cannot sleep.

Can thyroid problems cause insomnia?

Yes. Thyroid imbalance can affect metabolism, blood sugar, cortisol rhythm, heart rate, body temperature, anxiety, and nervous system activity. Many people with Hashimoto’s, Graves’ disease, hypothyroidism, or thyroid conversion problems also struggle with insomnia.

Can estrogen dominance cause insomnia?

Yes. Estrogen dominance and low progesterone can contribute to sleep problems, especially in women during PMS, perimenopause, menopause, or hormone transitions. Progesterone has a calming relationship with GABA activity, which is important for sleep.

Can blood sugar problems cause insomnia?

Yes. Blood sugar swings can trigger cortisol and adrenaline, especially during the night. This may cause waking at 2, 3, or 4 AM, restless sleep, night sweats, anxiety, or difficulty falling back asleep.

What testing is helpful for insomnia?

Helpful testing may include saliva cortisol rhythm, fasting glucose, fasting insulin, A1C, thyroid markers, inflammatory markers, sex hormones, DHEA, nutrient markers, and in some cases genetic or neurotransmitter-related testing.

Need Help Finding the Root Cause of Your Insomnia?

If you have tried melatonin, magnesium, sleep hygiene, prescription sleep aids, or relaxation techniques and you still struggle with insomnia, it may be time to look deeper.

Sleep problems are often a sign that something else in the body is out of balance. High nighttime cortisol, blood sugar instability, inflammation, thyroid problems, hormone imbalance, COMT gene variations, and nervous system dysregulation can all interfere with your ability to fall asleep and stay asleep.

At our office, we use a functional medicine approach to help identify the underlying patterns contributing to chronic sleep problems.

If you need help finding the root cause of your insomnia, schedule a free 15-minute consult with Dr. Hagmeyer to learn more about your next steps.

For Yoast, I’d use “root causes of insomnia” as the focus keyphrase, with secondary phrases like insomnia causes, trouble falling asleep, trouble staying asleep, high cortisol at night, blood sugar and insomnia, and hormone imbalance and insomnia.