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A Root Cause Medicine Protocol For Patients With Insomnia: Testing, Therapeutic Diet, and Supportive Supplements

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A Root Cause Medicine Protocol For Patients With Insomnia: Testing, Therapeutic Diet, and Supportive Supplements

According to the National Sleep Foundation, over one-third of adults do not meet the recommended amount of sleep, 7-9 hours per night. Insomnia is the most common sleep disorder, with 30% of adults experiencing short-term and 10% experiencing chronic insomnia. Lack of sleep seriously impacts health and quality of life, so diagnosing the reason for poor sleep and treating it accordingly is important. (12, 30


What is Insomnia?

Insomnia is a sleep disorder characterized by difficulty falling asleep, staying asleep, or experiencing poor quality sleep, despite having the opportunity and right environment conducive to good sleep. As a result, people with insomnia will wake up feeling unrefreshed and tired during the day.

Not all cases of insomnia are identical, and insomnia was previously categorized as primary or secondary, depending on the cause. Recently, however, this categorization system was changed so that the two main insomnia types are short-term and chronic. Short-term, or acute, insomnia lasts less than three months, is often caused by a stressful life event, and typically resolves on its own with time. Short-term insomnia may become chronic if the problem persists for at least three nights per week for three months or longer. Short-term and chronic insomnia can occur in people of all ages and is more prevalent in women. (24, 32

Insomnia Signs & Symptoms

You may have insomnia if you experience at least one of the following symptoms at least three times per week for at least one month:

  • Difficulty falling asleep
  • Inability to stay asleep, being awake for much of the night, and sleeping only for a short period
  • Early morning awakenings
  • Nonrestorative sleep: not feeling rested upon waking
  • Daytime impairment or distress associated with a lack of sleep

What Are The Possible Causes of Insomnia?

Insomnia has a long list of possible causes, including:

Circadian Rhythm Disruption

The circadian rhythm is a biological 24-hour cycle that regulates the timing of various physiological and behavioral human processes. The circadian rhythm is primarily controlled by the suprachiasmatic nucleus (SCN), a cluster of cells in the brain's hypothalamus. This internal "body clock" is synchronized with the external environment, mainly through the light-dark cycle, which helps maintain the proper timing of these processes. (1

Melatonin, known as the "sleep hormone," is produced by the pineal gland in response to darkness, increasing in the evening to signal winding down for sleep. Cortisol, associated with stress response, peaks in the early morning for alertness and gradually decreases throughout the day. The intricate interaction and regulation of these hormones by the circadian rhythm are disrupted in cases like shift work, jet lag, exposure to artificial light, or irregular sleep, potentially leading to insomnia. (1

Poor Sleep Hygiene

Poor sleep hygiene refers to a set of behaviors, habits, and practices that can disrupt the quality and quantity of sleep. Common examples of poor sleep hygiene include having an inconsistent sleep schedule; engaging in stimulating activities before bed; consuming caffeine, nicotine, and alcohol later in the day; taking long naps during the day; maintaining an uncomfortable sleep environment characterized by excessive noise, light, or an incorrect room temperature; using the bed for activities other than sleep; and consuming large, heavy meals too close to bedtime. Irregular exposure to natural light, or, in other words, lack of exposure to natural light during the day and excessive exposure to artificial light in the evening, can also disrupt sleep-wake cycles. (14, 15)

Stress & Anxiety

Emotional and psychological factors, such as stress, anxiety, and depression, can disrupt sleep patterns and make it difficult to relax and fall asleep. Chronic stress causes hypothalamic-pituitary-adrenal (HPA) axis dysfunction, characterized by abnormal cortisol secretion patterns that disrupt the sleep-wake cycle. Physical symptoms of stress and anxiety, such as rapid heart rate, shortness of breath, and ruminating thoughts, can also make it difficult to relax and fall asleep. (3)

Underlying Medical Issues & Medications

Insomnia can become more common as people age, often due to changes in sleep patterns and health conditions (15). Examples of medical conditions associated with insomnia include chronic pain, cancer, diabetes, asthma, gastroesophageal reflux disease (GERD), hyperthyroidism, post-traumatic stress disorder, menopause, and sleep apnea. (5, 14

Some medications, particularly those that affect the central nervous system, can also disrupt sleep patterns, causing insomnia as a side effect. Many anti-allergy and nasal decongestants contain stimulants. Beta-blockers used to manage high blood pressure deplete melatonin. Antidepressants can disrupt neurotransmitter balance, leading to changes in sleep patterns. Diuretics can deplete magnesium, which is involved in GABA production, and cause frequent nighttime urination. (9, 14)  

Functional Medicine Labs to Test for Root Cause of Insomnia

A sleep study is considered the gold standard evaluation for sleep disorders, so it is ordered for most patients reporting disrupted sleep patterns. During this overnight test, the patient's brain waves, blood oxygen level, heart and respiratory rates, and eye and leg movements are monitored to determine if, when, and why sleep patterns are disrupted. Additionally, an in-depth patient intake, ensuring to review past medical history, medication/supplement lists, and lifestyle habits, and lab work play valuable roles in getting to the root cause of insomnia.

Hormone Testing

There are several endocrine (hormonal) systems to consider and evaluate during a functional medicine evaluation of insomnia. When imbalanced, stress, reproductive, and thyroid hormones can contribute to poor sleep by disturbing the body's circadian rhythm and causing physical symptoms that can impair sleep quality.

As cortisol and melatonin are two hormones most strongly related to the sleep-wake cycle, sleep testing utilizes salivary samples to measure cortisol and melatonin levels throughout the day. When the natural diurnal rhythm of either hormone is disturbed, insomnia can occur. 

Insomnia is common in women experiencing hormonal shifts during the menstrual cycle, perimenopause, and pregnancy. Night sweats, hot flashes, and other hormonal symptoms can cause discomfort and disrupt sleep. Female sex hormones can be measured in blood and urine to detect imbalances. 

Both under- and overactive thyroid can contribute to insomnia, making a comprehensive thyroid evaluation an important aspect of laboratory investigation of insomnia. Abnormal patterns in TSH, T3, and T4 hormones are diagnostic for hypothyroidism and hyperthyroidism. 


Neurotransmitters are chemicals that transmit signals between nerve cells in the brain and throughout the nervous system. Imbalances in calming and excitatory neurotransmitters can cause the nervous system to be overstimulated, resulting in insomnia. Imbalances in glutamate, histamine, dopamine, GABA, and serotonin are often linked to insomnia. (10


Micronutrients are the vitamins and minerals used as cofactors for enzymes that catalyze the biochemical pathways responsible for energy, neurotransmitter, and hormone production. Deficiencies result in biochemical imbalances that can contribute to insomnia. Sleep duration is positively associated with iron, zinc, and magnesium and negatively associated with copper, potassium, and vitamin B12 (22). There is also evidence of an association between short sleep and inadequate intake of calcium and vitamins A, C, D, E, and K in women. 


Conventional Treatment for Insomnia

Treatment for insomnia can vary based on its underlying cause. It might involve addressing underlying medical or psychological issues, improving sleep hygiene (developing healthy sleep habits), making lifestyle changes, and, in some cases, using medication under the guidance of a medical professional. Cognitive-behavioral therapy for insomnia (CBT-I) is a common non-pharmacological approach that helps individuals develop better sleep habits and change negative thought patterns related to sleep. (29)

Functional Medicine Treatment Protocol for Insomnia

Given that no one specific cause of insomnia exists, functional medicine emphasizes an individualized treatment approach that starts by identifying the contributing factors to disordered sleep. Once these factors have been identified through history taking and specialty labs, functional medicine doctors will address those concerns with diet, lifestyle modifications, supplements, and, as indicated, medications. 

Dietary Interventions for Insomnia

Research indicates that dietary choices and patterns characterized by excessive calorie and sugar consumption, insufficient intake of fruits and vegetables, skipping breakfast, and irregular mealtimes are associated with insomnia. The American Academy of Sleep Medicine suggests that blood sugar fluctuations caused by high refined carbohydrate intake can also trigger insomnia. 

Taking these findings into consideration, along with the conclusions of another large-scale study, that revealed a greater consumption of dietary fiber, whole grains, fruits, and vegetables corresponded to a lower likelihood of experiencing insomnia, eating a healthy, whole-food, and low-glycemic diet is recommended for treating and preventing insomnia.

Need help knowing where to start in making dietary changes? Follow the DASH diet, a heart-healthy diet emphasizing whole grains, nuts, low-fat dairy, fruits, and vegetables. A 2019 study that included nearly 500 adolescent girls found that high adherence to a DASH-style diet was associated with a lower prevalence of insomnia. 

Natural Sleep Aids and Other Supplements for Better Sleep

Your doctor may recommend natural supplements as a first-line treatment option over prescription medications for insomnia. It is recommended that natural sleep aids be taken 30-60 minutes before bed. Research demonstrates that the following supplements are effective in improving sleep.


Melatonin is the fourth most popular natural supplement among American adults. Low nighttime melatonin levels, caused by exposure to light, aging, and diseases, can cause sleep disturbances. Research has shown that melatonin is an effective option in treating sleep disorders, including jet lag and delayed sleep-wake phase disorder. Supplementation improves sleep quality, sleep onset latency, sleep-wake patterns, and delayed sleep phase syndrome. (23, 26

Dose: 1-3 mg

Duration: 3 weeks


Valerian (Valeriana officinalis) root is the most studied plant for sleep disorders. Despite its pungent smell, often compared to dirty socks, valerian supplementation may improve sleep by up to 80% (31). Studies have shown that administering valerian before bed improves sleep quality, latency, and duration and reduces wake time after sleep onset. (11

Dose: 400-1,060 mg

Duration: 4 weeks

Lavender Oil

Silexan, an oral lavender oil capsule preparation, improves sleep quality and is as effective as lorazepam in treating generalized anxiety disorder in adults (11). Other studies using topical lavender essential oil showed similar effects, concluding that lavender oil improves sleep quality, especially when combined with good sleep hygiene practices.  

Dose (Oral): 80 mg 

Duration: 10 weeks


Magnesium deficiency is becoming increasingly prevalent, especially among older adults. Magnesium is believed to reduce insomnia by antagonizing NMDA receptors, the receptor for the primary excitatory neurotransmitter in the brain, and activating GABA, an inhibitory and calming neurotransmitter. Positive clinical outcomes of magnesium supplementation include improved sleep quality, duration, onset latency, and reduced early-morning awakenings. (26

Dose: 320-500 mg

*Note: at higher doses, magnesium may cause loose stool; if this occurs, decrease the dose to bowel tolerance.

Duration: 7 weeks

Relaxation for Sleep

Stress reduction through mind-body therapies, including breathing exercises, meditation, and muscle relaxation, can help put the mind and body in a relaxed and restful state conducive to falling and staying asleep. Yoga and meditation are evidence-based practices proven effective in reducing physical and psychological manifestations of stress, anxiety, and depression. Other studies show that people who have learned relaxation techniques can fall asleep more quickly and sleep longer through the night. (16, 20

Sleep Hygiene Habits

Adopting good sleep hygiene practices is important to manage insomnia related to circadian rhythm disruption. This includes maintaining a consistent sleep schedule, creating a conducive sleep environment, limiting exposure to bright light before bedtime, and avoiding stimulants like caffeine and nicotine close to bedtime. (5

When To Retest Labs

After the first month of the treatment protocol, follow-up is indicated to assess the patient's response, reorder labs, and modify the plan as needed. After that, follow-up at least every six months, or sooner as required, is recommended until the insomnia has resolved.

Learning More About Insomnia



Insomnia is a sleep disorder characterized by the inability to fall or stay asleep that affects most individuals at some point during their lives. A variety of different factors can cause insomnia. Your functional medicine doctor will work with you to identify the cause of insomnia and implement a multi-faceted plan that corrects the underlying imbalances related to hormonal, micronutrient, and circadian dysfunction.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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