The Surprising Connection Between Headache and Gut Health (Some May Surprise You)

People often ask, “Why am I getting a headache for no reason?” The truth is, there’s always a cause—it just requires some investigation. Your migraine might stem from one factor or a combination of factors – and a lot of times there’s a link between headaches and gut health. Ultimately, the question you want answered is, “How do I make my headache go away?!” Once you know your headache’s root cause, you’ll know exactly how to find relief.

Key Takeaways

• Most of the time, one or more of these 14 causes can explain why you have a headache. 
• Once you identify your headache trigger(s), they’re easier for you to manage.
• Many causes have simple solutions for headache reversal. For example, removing food sensitivities, drinking more water to prevent dehydration, and eating regularly to prevent low blood sugar can help.
• In some cases, additional testing with a functional medicine healthcare practitioner can help identify unique headache triggers.
• Natural treatments like ginger and magnesium are effective for helping headaches. Ginger is as effective as a popular migraine drug.

Table of Contents

Root Causes and Natural Remedies for Headaches and Migraines 

Chronic headaches are a common complaint we see at Aura Functional Medicine. As Naturopathic Doctors and Functional Medicine Practitioners, we are always looking to address the underlying cause of headaches and migraines and offer natural relief. We’ve identified the top 14 causes of headaches and natural remedies that help.

What is a dehydration headache?

Dehydration causes your blood volume to drop which in turn lowers blood flow and oxygen to the brain. Just as a sponge dries up and shrinks, your dehydrated brain puts pressure on surrounding structures causing headache pain.1 Women with migraines who drink around 2 liters of water each day experience decreased severity, pain intensity, headache frequency, and headache duration.2 

It is estimated that you need approximately half your body weight in ounces of water each day.  For example, a 150-pound person should aim for 75 ounces of water. You may need to increase this amount with increased activity and sweating. High-water content foods such as watermelon and cucumber also count toward your daily total.  

Food sensitivities as a headache trigger

Food sensitivities are a very important factor in chronic headache and migraine.3,4 

• Fermented and aged foods such as alcohol, cheese, vinegar, sauerkraut and kombucha are high in tyramine and histamine which can be problematic in some people. 
• The food additive monosodium glutamate (MSG) can have an “excitotoxin” effect and cause multiple neurological symptoms including severe headache. 
• Cured meats such as hot dogs, salami and bacon contain nitrites which can dilate blood vessels and lead to headache in sensitive individuals. 
• Interestingly, both caffeine consumption and caffeine-withdrawal can be a headache trigger due to its effect on blood vessels. 
• Gluten, a protein found in grains such as wheat, rye and barley has also been reported as a common headache trigger. 
• Some people are even sensitive to citrus fruits due to a stimulating compound called synephrine.  

Many times, food triggers are dose-dependent and vary by person. The best way to identify problematic foods is to do an elimination diet and carefully track food-reintroduction with a food and headache journal. The National Headache Foundation www.headaches.org has several helpful resources including food lists and a headache diary. There is also some evidence to suggest IgG food sensitivity testing can be helpful in identifying problematic foods in migraine sufferers.5-7  

Chronic infections triggering headaches

Chronic infections such as candida overgrowth and Lyme disease release inflammatory compounds that can lead to headaches. Headaches are triggered from “die-off” when overgrowth is treated.8,9 A functional medicine-trained healthcare practitioner can help to identify and treat these infections correctly.

Hormonal headaches

Headaches from hormone fluctuations and imbalances are common. For women, a balance between estrogen and progesterone is important. Many women are “estrogen dominant” due to a combination of stress, high-estrogen foods and chemicals in our environment that mimic estrogen. The sudden drop in estrogen just before a woman’s menstrual cycle is also a common headache trigger.10,11 

There are several diet and lifestyle interventions for hormone health: regular activity and exercise, avoidance of harmful chemicals, nutrient-rich diet including dark, leafy greens and brassica vegetables. Additional nutrients such as vitamin B6 are important for supporting estrogen metabolism.12 When appropriate, botanical medicine can also be used to support hormone balance. Working with your healthcare provider to assess for hormone imbalance, nutrient deficiency, and other lifestyle factors is important for a personalized wellness plan.  

Headaches from low blood sugar

Low blood sugar, or hypoglycemia, can lead to symptoms that may include headache, blurry vision, nervousness, fatigue, sweating, or rapid heart-rate. While low blood sugar can happen to anyone, especially if you’ve skipped a meal or done an intense workout without refueling, it may also be a sign of blood-sugar problems or insulin resistance.13   

Avoiding high-sugar foods and refined carbohydrates (think pasta, chips, bread, crackers and baked goods) while eating regular meals that contain adequate protein and healthy fat is very helpful for balanced blood sugar. If you have diabetes, low blood sugar can be dangerous.  Careful monitoring of blood sugar and medication management is important.  

Which medications and supplements cause headaches?

Medications and supplements can also be associated with chronic head pain. Any hormone therapy, including birth control pills can be a headache trigger.14 Over-the-counter pain medications such as aspirin and ibuprofen (NSAIDs) may initially be helpful for headache but can lead to a “rebound” effect and a worsening of pain.15 Even a supplement such as ginkgo, which is generally considered safe and thought to help headaches, can also lead to headaches due to its effect on blood vessels.16  

It’s important to discuss all supplements and over-the-counter medications with your healthcare provider. If you are taking any prescription medication and suspect a connection with your chronic headache, talk with your doctor. 

Nutrition and headaches

Nutrient deficiencies can also play a role in chronic headaches. Your cells need a variety of vitamins, minerals and other nutrients for healthy function. A standard American diet is largely deficient in many vital nutrients. There are also a number gastrointestinal conditions including IBS (irritable bowel syndrome), IBD (Crohn’s and ulcerative colitis), and SIBO (small intestinal bacterial overgrowth) that can decrease the ability to adequately absorb nutrients from the diet.  

There are several studies indicating benefit from improved diet and supplementation in the reduction of headache. Some of the nutrients studied include folate from green, leafy vegetables, B vitamins, especially Riboflavin (400 mg daily), magnesium (200-600 mg daily, CoQ10 (100-400 mg daily), and vitamin D (2,000-5,000 IU daily).17-21 While these vitamins are generally safe at the recommended doses, it is always a good idea to work with your healthcare provider to make sure you are not over-supplementing.   

Poor posture and tension headaches

Poor posture can put strain on the muscles of the head and neck, resulting in nerve irritation and tension headache.22 Many of us spend several hours a day hunched over a computer or looking down at our phones.  

Simple changes such as setting your phone or computer at eye-level can be very helpful for decreasing neck tension and strain. Targeted strength training, physical therapy, massage, chiropractic care and acupuncture can also be helpful to correct muscle imbalances and posture.  

Headaches from stress

Stress is one of the most commonly recognized headache triggers. When you are stressed, physiological changes such as inflammation, tense muscles, poor sleep, and improper breathing can all contribute to head pain.22 

We are all exposed to stressors daily. It’s important to know that you have the power to change your response to the stressor. There are several tools that can help us shift to a healthier response. Practices like deep breathing, biofeedback, HeartMath, meditation, yoga, tai chi, Qigong, and mindfulness can be life changing.  

How do you get rid of a headache from eye strain?

Eye strain is another common headache trigger. Many of us are staring at a computer screen or electronic device several hours each day. Blurry vision from not wearing glasses and bright lights can trigger headaches.23

It’s important to have proper lighting and take breaks. My optometrist recommends the “20-20-20 rule”. Every 20 minutes, take a 20-second break and focus your eyes on something at least 20 feet away. If you’re struggling with chronic headaches, it’s also important to have your vision checked regularly for eye muscle imbalance or vision problems.   

Allergies and sinus headaches

Allergies can cause sinus pressure and result in headaches. It’s important to identify and avoid the allergen when possible. Here are several tips for dealing with allergies:

• If you’ve been outdoors and allergens such as pollen are an issue, you can minimize exposure by taking your shoes off at the door, changing your clothes and washing your hair before bed. 
• Mold can be especially problematic for some individuals. The American College of Allergy, Asthma and Immunology (ACAAI) recommends keeping the humidity in your home between 30 and 50 percent to limit mold. Cleaning bathrooms, kitchens and basements regularly while utilizing a dehumidifier for damp areas also helps decrease mold. 
• Using a HEPA vacuum and air filter can also be helpful for trapping particles such as pollen, pet dander, dust mites, mold spores and some bacteria and viruses. 
• Natural treatments to decrease an allergic response include vitamin C, quercetin, stinging nettle and ginger to name a few.24 
• Consuming an anti-inflammatory diet is one of the best ways to combat allergies. For example, fruits and vegetables contain vitamin C, quercetin, and other anti-inflammatory compounds. 
• It’s also important to note that some herbs and foods can cross-react with certain types of pollen. For example, those with an allergy to grass may also notice symptoms when eating melon, orange, peanuts, or tomatoes.25 
• Utilizing a neti pot or saline spray to flush the sinuses can also be helpful for allergy sufferers.     

Are migraines genetic?

Genetic susceptibility is another consideration in chronic headache. Dozens of genetic variants have been associated with chronic headache and migraine. With the availability of affordable genetic testing through companies like 23andMe, obtaining your own genetic information has become rather easy. Single nucleotide polymorphisms (SNPs) are common genetic variants that can influence a variety of traits such as appearance, disease susceptibility or response to drugs. The study of these SNPs and how they affect your health is a relatively new area of research. Genetic SNP information can provide some helpful information, but we still have a lot to learn.  

The genetic variant for methylenetetrahydrofolate reductase (MTHFR) has been getting a lot of press lately. The MTHFR enzyme plays a very important role in the utilization of folate. Having one or more “bad copies” of this gene can contribute to multiple health-related issues including headache, migraine, trouble with detoxification, difficulty breaking down histamine, neurotransmitter (dopamine, serotonin, norepinephrine) imbalance, elevated homocysteine, and cardiovascular issues.26-28 While MTHFR SNPs and folate get a lot of attention, it’s important to know that they are only one piece of the puzzle. There are several other genetic SNPs, nutrients and lifestyle factors involved in these biochemical processes.    

Your body is very dynamic and has many checks and balances in place to overcome health challenges. It’s also important to know that your genes are not your destiny. There are several factors that affect how your genes are expressed such as nutritional status, infections, toxin exposure, gut health, exercise and stress management. If you suspect a genetic connection with your chronic headache or migraine, it’s best to work with a healthcare provider that is knowledgeable on the subject.  

Can constipation cause headaches?

Constipation and headache can occur together for several reasons. First, you reabsorb toxins and hormones meant for elimination when constipated. There are also common underlying causes for both headache and constipation such as magnesium deficiency and dehydration.  Food sensitivities, especially to gluten, have been linked with constipation and headache.29  Conditions that affect our nerves such as Multiple Sclerosis and Parkinson’s are also linked with both headache and constipation.30,31 The stress, discomfort, and straining associated with constipation can also contribute to headache.  

Much like chronic headaches, constipation is multifactorial. It’s always important to start with lifestyle basics such as drinking enough water, addressing nutrient deficiencies, and eating a fiber-rich diet with healthy fats. Exercise and activity are also important for encouraging healthy bowel movements. Finally, addressing underlying disorders that slow gastrointestinal motility such as SIBO-C, hypothyroidism, and neurological disorders is also extremely important.  

Headaches from chemical and toxin exposure

Toxic exposure is another trigger for headache and migraine sufferers. Each day, you are exposed to multiple chemicals and scents found in perfumes, personal care products, cleaners, air fresheners, candles, building materials, paint, fabrics, furniture, carpeting, clothing, food additives, preservatives, pesticides, and more.

Thousands of new chemicals are introduced into the environment with very little regulation or study on long-term health effects.32 The US Environmental Protection Agency admits that even if each chemical were to be thoroughly tested, we still have no idea what happens when these chemicals interact with each other.

With the large number of daily chemical exposures, it can be difficult to know where to start.  

• When possible, buy non-toxic, environmentally conscious products and do your best to keep windows open for fresh air.  
• Indoor plants such as ferns and palms are great natural air cleaners.  
• Avoid using pesticides on your lawn and buy organic food and products when possible.  
• Fortunately, there are good resources to help you reduce your chemical exposure. The Environmental Working Group www.ewg.org has a lot of helpful information and a “Healthy Living” phone app that allows you to scan and browse various products for safety ratings. 

Quick tips for headache relief

While working to address the underlying cause of a person’s headache, symptomatic relief is still important. One of my favorite ways to stop a headache or migraine in its tracks is to consume a 1-inch piece of fresh ginger (chopped or juiced) or ½ teaspoon dried ginger. One study found ginger to be as effective as the powerful migraine drug, sumatriptan!33 Taking 150-200 mg of magnesium along with the ginger may provide an even greater reduction in headache. The ginger or ginger- magnesium combination may be taken every 2-4 hours as needed.

Some people are also helped by using a cold washcloth or ice pack on the back of the neck or forehead while simultaneously submerging their feet in very warm water. This can provide symptomatic relief by drawing blood-flow away from the head and down toward the feet.  

When to worry about a headache

Important: A “first or worst headache” that is unusually severe or lasts more than a couple of days should be checked by a doctor. Seek emergency medical care for any headache that is accompanied by fever, stiff neck, paralysis, or confusion.  

Seeking help for your headaches

In my clinical experience, chronic headaches and migraine are often the result of multiple factors. With so many potential headache triggers, it can be difficult to know where to start. A great first step is to avoid the common trigger foods listed at www.headaches.org. While addressing dietary triggers and nutrient deficiencies can be helpful for some, others may benefit from functional medicine testing to uncover whether they have headaches from hormones, hidden infections, or genetic predispositions.  

Frequently Asked Questions

What is the difference between headaches and migraines?

There are several types of headaches with migraines being one of the most severe types. In addition to headache, people with migraines may also have nausea, light, sound, or smell sensitivity, dizziness, extreme fatigue, blurry vision, and may also see an aura or light haze before the migraine appears. Many of the headache causes listed in this article can trigger many types of headaches. 

Does the type of headache and location matter?

People get headaches on top of the head, back of head, on temples, right and left side of head – these locations can tell you something about the cause, but it’s best to have a comprehensive look at all headache causes rather than limit to one possibility based on location.

What causes headaches everyday?

Any of the causes listed in the article could cause daily headaches. Sometimes people have more than one trigger. Consider each cause and troubleshoot to see if that resolves your daily headaches. If not, consider a visit with a functional medicine practitioner to help you uncover the root cause of your daily headaches.

What are natural treatments for headaches?

Ginger and magnesium work great for headaches. It’s best to learn the underlying cause – once the cause is dealt with, headaches will often resolve on their own.

There are several types of headaches with migraines being one of the most severe types. In addition to headache, people with migraines may also have nausea, light, sound, or smell sensitivity, dizziness, extreme fatigue, blurry vision, and may also see an aura or light haze before the migraine appears. Many of the headache causes listed in this article can trigger many types of headaches. 

People get headaches on top of the head, back of head, on temples, right and left side of head – these locations can tell you something about the cause, but it’s best to have a comprehensive look at all headache causes rather than limit to one possibility based on location.

Any of the causes listed in the article could cause daily headaches. Sometimes people have more than one trigger. Consider each cause and troubleshoot to see if that resolves your daily headaches. If not, consider a visit with a functional medicine practitioner to help you uncover the root cause of your daily headaches.

Ginger and magnesium work great for headaches. It’s best to learn the underlying cause – once the cause is dealt with, headaches will often resolve on their own.

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