Bread on table next to wheat and other gluten-containing food that can cause headaches

Can Gluten Cause Headaches?

Medically reviewed on December 10, 2023 by Jillian Foglesong Stabile, MD, FAAFP. To give you technically accurate, evidence-based information, content published on the Everlywell blog is reviewed by credentialed professionals with expertise in medical and bioscience fields.

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Gluten, a protein that’s found in wheat, barley, and rye, negatively impacts about 6% of the U.S. population. This means that over twenty million people have a gluten intolerance.[1] For these people, eating gluten can cause bloating, gas, and abdominal pain, among other common symptoms.[1]

That said, can gluten cause headaches in people who are gluten intolerant?

Yes, headaches are a fairly common symptom of gluten intolerance, as well as celiac disease, which occurs when the immune system attacks gluten in the small intestine.[2]

Understanding Gluten Intolerance vs. Celiac Disease

Gluten intolerance and celiac disease are two separate conditions. If you’re experiencing headaches after eating gluten, it’s important to understand their differences.

Gluten Intolerance Symptoms

The exact cause of gluten intolerance is still up for debate. It’s believed that some digestive systems cannot properly digest carbohydrates, and as a result, these food particles stay in the stomach and intestines, where they eventually ferment and cause discomfort and sickness.[1]

Other research points to the lining of the small and large intestines. Does gluten cause inflammation? People who have a gluten intolerance may also have weak intestinal lining that leaks bacteria into the blood and/or liver, causing inflammation.

People with a gluten intolerance can experience:

  • Abdominal pain
  • Anemia
  • Anxiety
  • Bloating
  • Gas
  • Brain fog
  • Depression
  • Diarrhea
  • Constipation
  • Fatigue
  • Joint pain
  • Nausea and/or vomiting
  • Skin rash
  • Headaches

While the direct tie between gluten and headaches is not fully understood, a 2021 review found that a gluten-free diet can reduce migraine and headache frequency in some people.[3]

That said, headaches are more commonly prevalent in patients with celiac disease.[3]

Celiac Disease Symptoms

Celiac disease affects 1 in 100 people worldwide, but only 30% of these people have a diagnosis.[4] It is especially common among people with certain conditions, such as Hashimoto's thyroiditis.

When people with celiac disease eat gluten, their immune system will attack their small intestine. As time goes on, immune cells can damage and erode the lining of the small intestine, hindering the proper absorption and dispersion of nutrients. This can, in turn, cause nutritional deficiencies. As a result, people with celiac disease can experience [3,6]:

  • Weakness and fatigue
  • Pale complexion
  • Cold hands
  • Brittle nails
  • Mouth sores
  • Weight loss
  • Growth delays (in children)
  • Low muscle tone
  • Dental enamel erosion
  • Abnormal periods
  • Mood changes

When the small intestine becomes damaged, people can also experience such gastrointestinal issues as [3,6]:

  • Diarrhea
  • Fatigue
  • Weight loss
  • Bloating
  • Anemia
  • Stomach pain
  • Fatty stools

Of course, symptoms also include headaches and/or migraines.[6] It’s believed that the connection between celiac disease and headaches lies in the gut-brain axis, in which the brain and digestive system communicate. This axis plays a crucial role in various physiological processes that involve inflammation and immune responses.[7]

Migraines occur when the body releases inflammatory and vasoactive mediators, which impact the blood vessels in the brain. It’s further believed that the gut microbiota influences immune responses and the workings of the nervous system. While the exact mechanism that connects celiac disease to migraines is still unknown, research does conclude that there is an impact.[7]

Further, Beyond Celiac reports that people with celiac disease who started a strict gluten-free diet experienced fewer migraines, and when migraines did arise, they were less painful.[8]

If you suspect that gluten may be causing your headaches, consider the following tactics:

  • Eliminating gluten from your diet entirely
  • Keeping a food diary to assess what types of food trigger your symptoms

If you’re experiencing headaches after eating products made with wheat, barley, or rye, and you’ve yet to be diagnosed with a gluten-related condition, visit your healthcare provider to discuss your symptoms.[1,6]

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Your healthcare provider will likely ask you to adhere to a gluten-free diet, and then perform blood tests and skin tests to rule out a gluten allergy or celiac disease. If you do have celiac disease, you may have gluten antibodies in your blood—though in some cases celiac disease has to be diagnosed endoscopically.

Your healthcare provider can also assess gastrointestinal damage by taking a biopsy of the small intestine through an endoscopic procedure.[1,6]

If you do have a gluten intolerance, it’s important to understand that there is no cure. However, you can manage the condition with a strict gluten-free diet, which can help reduce symptoms, including headaches. Your healthcare provider may also recommend adding probiotics to your celiac diet plan to support your gut health and digestion.[1]

To treat neurological symptoms like the headaches or migraines caused by celiac disease, you must address the root issue. In addition to maintaining a strict gluten-free diet, your celiac treatment may include [6]:

  • Adding supplements to your diet to increase nutrient intake
  • Taking corticosteroids to reduce inflammation

Learn More About Your Health With Help From Everlywell

It’s common for people with a gluten intolerance or gluten inflammatory response to also experience headaches or migraines. Fortunately, you can mitigate the frequency and severity of your symptoms by following a strict gluten-free diet.

If you’re looking to learn more about your nutritional health, try an at-home test from Everlywell. Our Celiac Disease Screening Test, in particular, checks for antibodies that may indicate a celiac diagnosis. Or, try out our Food Sensitivity Test, which measures your body’s immune response to 96 different foods to support an elimination diet. Once you receive your lab-reviewed results, we can connect you with a telehealth provider who can help determine the best course of treatment for you.

Explore our collection of at-home test kits or schedule a telehealth appointment today to get started.

What Causes Headaches After Eating?

What Causes An Upset Stomach After Eating?

Burning Sensation In Stomach: Causes & Treatment


  1. Gluten Intolerance. Cleveland Clinic. Published June 30, 2021. URL. Accessed November 13, 2023.
  2. Celiac Disease. Mayo Clinic. Published September 12, 2023. URL. Accessed November 13, 2023.
  3. Gabrielli M, et al. Migraine as a Common Extra-Intestinal Presentation of Celiac Disease. OBM Neurobiology. Published February 9, 2021. URL. Accessed November 13, 2023.
  4. What is Celiac Disease? Celiac Disease Foundation. URL. Accessed November 13, 2023.
  5. Celiac Disease. Mayo Clinic. Published September 12, 2023. URL. Accessed November 13, 2023.
  6. Celiac Disease. Cleveland Clinic. Published December 1, 2022. URL. Accessed November 13, 2023.
  7. Qasim H, et al. Dysbiosis and Migraine Headaches in Adults With Celiac Disease. Cureus. Published August 24, 2022. URL. Accessed November 13, 2023.
  8. Celiac Disease and Migraines. Beyond Celiac. URL. Accessed November 13, 2023

Jillian Foglesong Stabile, MD, FAAFP is a board-certified Family Physician. Since completing her residency training in 2010, she’s been practicing full-scope family medicine in a rural setting. Dr. Foglesong Stabile’s practice includes caring for patients of all ages for preventative care as well as chronic disease management. She also provides prenatal care and delivers babies. Dr. Foglesong Stabile completed a teaching fellowship in 2020 and teaches the family medicine clerkship for one of her local medical schools. Dr. Foglesong Stabile’s favorite thing about family medicine is the variety of patients she sees in her clinical practice.

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