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Celiac Disease and Headaches

I’ve been intending to write about the association between celiac disease and headaches over the last month, but every time I’ve sat down in front of my computer to start to write this post, I’ve given myself a headache :)

Seriously, though, I have had a lot of readers ask about whether or not headaches can be a symptom of celiac disease. Although I’ve always answered “yes,” because headaches are always on the lists of celiac symptoms, I had not dived into any of the research about this subject until now.

One of the first studies regarding celiac disease and headaches was published by a group of researchers from Columbia University in 2013.  The study group included 188 subjects with celiac disease and 25 subjects with non-celiac gluten sensitivity (NCGS).  Chronic headaches were reported by 30% of those with celiac disease and 56% of those with NCGS, while only 14% of the control group (n=178) reported having chronic headaches. A significant proportion of celiac subjects with chronic headaches also met criteria for having migraines.  The authors speculate that widespread inflammation and/or celiac antibodies attacking the nervous system may cause headache symptoms.

There was a larger scale study examining the association between celiac disease and headaches that was published earlier this year.  28,648 Swedish subjects with celiac disease were compared to 143,126 controls. The risk of headaches in subjects with celiac disease was significantly higher than in the controls (4.7% v 2.9%).  Interestingly enough, the investigators also found that subjects with elevated celiac antibodies but normal small intestinal biopsies (aka “potential” celiac) as well as subjects with intestinal inflammation, but not villous atrophy (the classic abnormality on small bowel biopsy in celiac disease), were also at a higher risk of having headaches.

Although the first two studies involved only adult patients with celiac disease, there has been some research showing an association between celiac disease and headaches in the pediatric population as well. The first was a well-designed Italian study published in 2009. 354 children with celiac disease were compared to 200 healthy controls. Almost 25% of the children with celiac suffered from headaches prior to their celiac diagnoses compared with only 8% of those without celiac.  Over ¾ of the children with celiac disease and headaches reported an improvement in headaches after going onto the gluten-free diet.  In addition, 5% of the control children with chronic headaches were found to have undiagnosed celiac disease. In another recent study a large sample of children attending a clinic for pediatric headaches were screened for celiac disease.  The prevalence of celiac disease in the children with chronic headaches was found to be twice as high as the general population (2.04% v 1.2%).

Some hypotheses regarding the link between celiac disease and headaches include that celiac-induced inflammation may spread to the brain and nervous system, that TTG antibodies can attack the nervous system, that they may be the result of long-standing vitamin deficiencies (i.e. B12, D, E, folic acid, and pyridoxidine) and/or lower than normal levels of serotonin, or might be due to an alteration of the microbiome (bacterial imbalance in the body).

In conclusion, there has been some solid research over the last few years that those of us with celiac disease have a higher risk of headaches than the general population, that patients with chronic headaches should probably be screened for celiac disease, and that following the gluten free diet may help to alleviate headache symptoms.

Have any of you with celiac disease or gluten sensitivity suffered from recurrent headaches either before or after diagnosis? If so, please feel free to share your story, as it will likely help a future reader. Thank you!

Happy End of Celiac Awareness Month too!



Dimitrova, AK, Ungaro, RC, Lebwohl, B, Lewis SK, Tennyson, C, Green, M, Babyatsky, MW, and Green, P.  (2013), Prevalence of Migraine in Patients with Celiac Disease and Inflammatory Bowel Disease. Headache: The Journal of Head and Face Pain, 53: 344-355.

Lebwohl, B, Roy, A, Alaedini, A, Green, PH, Ludvigsson, JF. Risk of Headache-Related Healthcare Visits in Patients with Celiac Disease: A Population-Based Observational Study.  Headache, Epub ahead of print on Mar 12, 2016.

Lionetti, E, Francavilla, R, Maiuri, L, et al. (2009), Headache in Pediatric Patients with Celiac Disease and its Prevalence as a Diagnostic Clue.  Journal of Pediatric Gastroenterology and Nutrition, 49(2): 202-207.

Nenna, R, Petrarca, L, Verdecchia, P, at al. (2016), Celiac Disease in a Large Cohort of Children and Adolescents with Recurrent Headache: A Retrospective Study.  Dig Liver Dis, 48(5): 495-498.

13 thoughts on “Celiac Disease and Headaches

  1. Julie Hahn

    Only every few years would I get a headache, most of my life. Now I get “ice pick” headaches that come on so suddenly, lighting bolt seems like a better name. Fortunately, they go away fairly quickly as well.

    In the last month I had a pill cam “procedure”. My small intestines are totally healed. Stem to stern, so to speak. That was excellent news.

    Like you, I’ve suffered with neurological problems from CD. Since I’ve been strictly GF since Jan 2009 and have worked hard at eating clean, anti-inflammatory and nutrient dense diet for most of those years, I feel mostly good. I do take a sublingual B-12 and D3, plus a good quality multivitamin/mineral daily.

    I would love to know if the headaches CD patients are experiencing are a result of inflammation or something else. I think the link to most of all chronic illness is inflammation. But I’m not the doctor.

    1. Jess Post author

      Hi Julie,

      My sister-in-law was just diagnosed with “ice pick” headaches as well and they sound awful, I am sorry you have had to go through this. That is wonderful news about your intestines being healed–congratulations :)

      My intuition tells me that my neuropathic symptoms are inflammation related, as I get diffuse inflammation throughout my body after I am glutened, but you are totally correct about inflammation being the common thread woven through most, if not all, chronic diseases like ours.


  2. shannon

    Thanks for this write-up Jess…. I was hoping that my diagnosis and subsequent gluten free life would make my headaches go away as it has with others that I have read about. My migraines are certainly not as severe or as frequent but definitely still a significant issue. I spoke with my neurologist about it and he simply said “why can’t you have migraines AND celiac disease?”. I also feel that there is a myofascial/musculoskeletal component as well. After many years of poor/lack of nutrition, it is not surprising to have long-lasting effects.

    1. Jess Post author

      I totally agree with you Shannon about the long-lasting effects of poor nutrition. I just replied to Kathleen, and it sounds like she has a similar experience of having just a minor improvement in headaches. I hope that there’s more research into this area and WHY (just like the need for research into almost everything else).

  3. Kathleen

    After a lifetime of undiagnosed Celiac, I developed chronic, life ruining migraines only two years prior to diagnosis. Going GF helped, but going from 20 incapacitated days to 15 a month doesn’t make my health that much more reliable. I can’t help but think that if my Celiac had been diagnosed earlier my life would be completely different.

    1. Jess Post author

      Hi Kathleen,
      I really appreciate that you shared your experience and I wish that you were not suffering like this.
      Have you experienced any other neurological symptoms associated with celiac? I have been interested in learning more about this topic because I developed a peripheral neuropathy, after my diagnosis.

      1. Rebecca

        Peripheral neuropathy can be related to B6 deficiency. Also, people with chronic illnesses can tend to have a difficult time properly absorbing the B complex vitamins, especially the top 3: Folate, B12 and B6, so trying to force more in by extra supplementation can actually cause problems like nausea and vertigo. (I know this from personal experience).

        So I am able to tolerate a small amount of a well absorbed B complex (about 1/16th of a capsule per day, and the bottle says to take 2 capsules per day) (I use the Emerald brand B Healthy B complex, but as I said, take only 1/16th of a capsule per day (any more is too much) because of my malabsorption issues (CBS 699 homozygous, MTHFR 1298 hetero, 2 homozygous ACE deletions, etc)

        At any rate, like anyone who cannot easily absorb anything (whether b vitamins or money), the only way I am able to keep my stores up properly (eg: save my B6/ “money” ) is to save it up and avoid things that “spend” it.

        I avoid all long chain saturated fatty acids because they deplete B6. (B6 and Lysine is used to catabolize and break down long chain saturated fatty acids.) I do eat olive oil and coconut oil (which is ok since it is only a medium chain fatty acid and so is a small enough molecule that it does not need to be broken down by either Lysine or B6)

        I also avoid foods high in oxalic acid because oxalic acid is toxic and the body uses B6 to convert it into a nontoxic form. I know that supposedly steaming or cooking things high in oxalic acid is supposed to render it non toxic, but I am so sensitive that I do get bothered by these foods, so I just avoid them.

        And the other thing I avoid like the plague is MSG and msg chemicals like “autolyzed yeast extract” and “hydrolyzed soy protein”, “natural flavorings”, “enzymes” etc which are all pretty much chemically msg. Glutamate chemicals can really suck up B6 stores since the body uses B6 to convert excess glutamate (excitatory neurotransmitter) to GABA (calming neurotransmitter). If you are B6 deficient, then you can get a bad chemically mediated migraine (like I do) just by small exposures to any glutamate chemicals (even tomatoes since they are naturally high in glutamate). (Electrically mediated headaches are caused by excess cellular calcium since calcium in excess can raise cellular electrical firing from a normal of 7 millivolts to 9 millivolts and above. Supplementation with a well absorbed magnesium, like ionic magnesium chloride liquid can help offset this by keeping excess calcium out of cells and also keeping the electrical firing of the cell down to its proper level of 7 millivolts. Calcium raises the electrical firing of cells to a point that can cause cell oversensitivity which can be registered as pain and magnesium chloride calms the electrical firing of the cell, so the whole system calms down.)

        In addition, supplementation with magnesium can help with neuropathy from magnesium’s own actions inside the cell and magnesium supplementation can also help with improving the body’s ability to absorb B6.

        Thankfully after my micro supplementation with the Emerald B Healthy capsules, I can now eat tomatoes again without feeling dizzy and nauseous.

        It has been my personal experience, from being a type 1 diabetic for 35 years that I only get neuropathy if I do something to deplete my B6. If I eat butter or a fried food, my toes usually get numb within 15 – 30 minutes of ingestion. If I avoid those foods and stay on my diet, I never have neuropathy.

        At any rate, if anyone is experiencing neuropathy issues, it might be a good idea to think about what you have eaten and if you might just be experiencing symptoms of a B6 deficiency.

        And for more info about magnesium and magnesium supplementation, a good book is “The Magnesium Miracle” by Dr. Carolyn Dean. You can also watch her on youtube. Another good book is “Excitotoxins:The Taste That Kills” by neurosurgeon Dr. Russell Blaylock, whom you can also watch on youtube. And, last but not least, a good book about the problems excess cellular calcium can cause: “The Calcium Lie: What Your Doctor Doesn’t Know Can Kill You” by Dr. Robert Thompson. He can be watched on youtube as well.

  4. Julie

    I was a lifelong migraine sufferer. When I went through menopause, they have been less frequent. Then, after being diagnosed with celiac disease at age 62, I now have what my ophthalmologist calls “ocular migraine.” I get the aura, but not the pain. It goes away after 1/2 hour with or without medication, but I feel exhausted as if I had a full blown migraine. I don’t know if the decrease and change in my migraines is related to menopause, celiac, both, or neither. My celiac symptoms, other than anemia, were a little weight loss, osteopenia, bone and joint pain, some depression, and major anxiety and panic attacks. I am a fiercely strong lady, so the anxiety and panic attacks when driving, have been very difficult to deal with. I still have them, even after being GF for 3+ years. I will keep trying to overcome them without any medication and get back my normal pre-celiac life.

  5. Dot

    I went GF over a year ago due to arthritis. It was suggested to me to try by a nurse caring for my mother several years ago. I have recently broken my GF diet. My headaches are horrible. I have to confess that I did not make the connection until just reading your article. While I have not been diagnosed with Celiac disease seeing the reference to both the GF and headaches gave me thought to comment in hopes the information I provided may help someone else.

    I am returning to my GF lifestyle A.S.A.P.!

    My best to you all.

    1. Jess Post author

      Hi Dot,

      I hope you feel better after you return to being GF.
      One thing I’ve come to appreciate is that if we ignore our body’s subtle signs that they usually get worse and worse until we finally listen :)
      Thanks for visiting my page and sharing your experience.


  6. Leslie

    I have had seasonal allergies since I was 12. I recently spent two years with a chronic mild headache…some days worse than others. I could count on my 2 hands my headache-free days over that time. I was told I had chronic allergic sinusitis. About to loose my mind with having these constant annoying headaches I finally went to the allergist to be tested and to possibly return to getting desensitizing shots (it had been 10 years since last completing treatment) . To my surprise I didn’t test positive for anything!
    Shortly after that I became very ill and ended up with my Celiac diagnosis. Within a couple days of starting a gluten-free diet I realized I didn’t have a headache. They were gone, completely gone! (My painful knees and ankles blamed on arthritis completely disappeared as well.)

  7. Andrea Robertson

    I have multiple food sensitivities that continue to get worse. I get stabbing pains and itching which I have been told is peripheral neuropathy. I do not have any intestinal issues, just neuro. I am seeing a functional neurologist and have done an elimination diet and supplements. I have some hormone deficiencies. The Doctor now suspects mold illness causing hypothalamic inflammation. Has anyone had this problem? I have celiac and am gluten free. I now react to most beverages, tomatoes, dairy, caffeine, all fruit. The symptoms last about 24 hours. Thanks for any suggestions.

  8. Rebecca Danis

    Hi, Andrea, I am so sorry to hear of your troubles. You most likely have MTHFR mutations (1298 or 677) and you might have some others as well including CBS mutations. First thing, I would suggest you get your genes mapped to find out the root genetic cause of your problems.

    I don’t have celiac, but at the height of my illness, I became allergic to many things. I am type 1 diabetic and I even became allergic to my insulin. This is because my B6 levels and Folate levels had dropped really low so my body was unable to make the calming neurotransmitters that help to prevent autoimmune issues like allergic reactions. Also because of the B6 and Folate deficiencies, this affected my liver so I could no longer metabolize chemicals very well. ( I have MTHFR and CBS as well as 40% of my genes being mutated)

    At any rate, if you have a CBS mutation, you should be avoiding all sodas or any sugary beverages that are not natural juices and even with natural juices, you should be sparing on those. And you should totally avoid dairy and caffeine like the plague as they are both very high in sulfur and phosphorus and with a CBS mutation where the body cannot properly break down sulfur and phosphorus, those foods will make you extremely ill.

    Or you might have a mutation which causes you to be sensitive to milk, but since coffee and black tea (which is also high in sulfur and phosphorus) is making you ill, I would suspect CBS mutation.

    The peripheral neuropathy you are also experiencing could be due to this as well. Peripheral neuropathy is caused by severe B6 depletion and CBS people have trouble absorbing B6 properly from foods. So they can suffer from many things relating to severe B6 deficiency.

    At any rate the best thing to do right now is get a gene mapping from 23andme dot com and also first visit the site genetic genie dot org because it will give you more information on getting your genes mapped.

    Allergies of any sort point to trouble in the processing (methylation) of the liver and this points to genetic mutations that affect methylation like MTHFR mutations, which prevent the body from properly absorbing folic acid and converting it into folate.

    So folic acid must be avoided (breads and cereals have it already added) and folate levels (folate is the broken down form of folic acid) must be raised by eating low sulfur, low phosphorus foods that are high in folate like organic romaine lettuce and oranges. (at this point though you might be too allergic to oranges, (I was too for a while) so just try a half a leaf or so of organic Romaine lettuce.

    So get your genes mapped to see what is behind these issues and get some organic romaine lettuce and it would be good to start slowly supplementing with liquid magnesium chloride as all these conditions cause severe magnesium deficiency.

    Do not take magnesium oxide as it is not well absorbed at all. The product I use which has worked very well for me is Trace Minerals Research “Mega Mag” liquid ionic magnesium chloride. The USRDA for magnesium is 400mg per day, but I would start out with 50-100mg per day and build up since you are so sensitive right now.

    This Trace Minerals Research “Mega Mag” is a pure liquid magnesium mineral and it comes in a blue bottle with a dropper. You can order it online. A four ounce bottle is about $13 and will last you for two months if you are taking the USRDA of 400mg per day, so the first bottle should last you a bit longer since you will be taking less magnesium chloride than the USRDA suggests.

    One dropperfull is equal to 100milligrams, so for you, to start, I would try 1/2 dropperfull(50mg) in a little orange juice (about 1 or 2 Table spoons/ 1/4 shot glass size) This stuff works great and will most definitely help with any mutations you might have and your food sensitivities, but as a liquid mineral it doesn’t taste so good, so just put a little OJ or other natural juice you can tolerate and then add the 1/2 dropperfull (50mg) to it and shoot the whole thing back. Doing it like that, it’s easy as pie. And it will really help calm your allergic immune response down. (after starting with 1/2 dropperfull, you can gradually build up to 1 dropperfull in am and 1 in pm and then build up to 2 in am and 2 in pm for a total of the USRDA of 400mg)

    Also, I would avoid any calcium or vitamin D supplementation, as both will increase sulfur and phosphorus levels in your body and rile up your immune system, especially if it is already over reactive like yours is and having lots of food sensitivities. I remember when I had that and it sucked! and it was so totally scary when I started having reactions to the insulin I have to inject every day to stay alive.

    At any rate, I took the magnesium chloride liquid every single day and I still do and my body gradually got more strong and I stopped having the severe food reactions and I didn’t get rashes or sick anymore when i took my insulin.

    When a person is low in magnesium chloride and B complex vitamins, esp B6, Folate and B12, the body cannot make the calming hormones/neurotransmitters like serotonin and GABA to calm down the immune system and the immune system can just fly out of control and develop all sorts of weird allergies to everything. As for the B complex, you should wait on that until you have been taking the magnesium chloride for a while. According to Dr. Robert Thompson who wrote “The Calcium Lie: What Your Doctor Doesn’t Know Could Kill You”, if you are deficient in your mineral levels, esp magnesium chloride, you won’t be able to properly absorb your vitamins, esp B Complex vitamins.

    (In order to equalize the other minerals, just get some Sea Salt which is balanced in all trace minerals.) After you have been taking the magnesium for a couple weeks or so, you should be ok to take a good well absorbed B complex vitamin with Folate in it instead of folic acid (folic acid is toxic for persons with MTHFR mutations) Folate is the more well absorbed form of folic acid and is best for everyone.

    A good well absorbed B complex vitamin is Emerald B Healthy with Methylfolate instead of Folic Acid. You can also order that off the net. The bottle suggests taking 2 capsules per day, but it sounds like your system is sensitive like mine and so I would recommend only taking about 1/8th of 1 capsule per day like I do and that is enough. If you find you need more, you can always take more, but that is what I would recommend.

    If you do the math on it, you will see that 1/8th – 1/16th of 1 capsule is pretty close to 100% RDA. 2 capsules is about approx 2000% of the RDA, and that is way too much especially since most deficiency problems occur because the body cannot properly metabolize the Bs, not because it is not getting enough.

    Throwing more B complex at someone whose body is a weak metabolizer in order to push more Bs into them, makes just about as much sense as forcing a 98lb weakling to Bench press 200lbs. It just can’t be done.

    I love this Emerald B complex in the small amount I take, but if I take 1 whole capsule, it makes me so amped up that I can’t sleep at night. So do what I do and take about 1/16th to 1/8th capsule. (just twist and open the capsule and use the sides of the capsule like little cups and pour in about 2 mm -4mm (millimeters) worth and take it with the liquid magnesium chloride and then reclose the capsule til the next day.

    You could also try taking a good well absorbed capsule of Vitamin C with bioflavanoids (just make sure it is not buffered because then that will have calcium and phosphate and will make your body more reactive and have more allergic reactions)

    Anyway, I bet you didn’t plan on this deluge of information, but I hope this helps :)

    Gene mapping ( MTHFR/ CBS mutations genetic genie dot org/ 23andme dot com)
    Magnesium chloride (50mg/day Trace Minerals Research “Mega Mag” liquid ionic magnesium chloride)
    Romaine Lettuce (for folate)
    Avoid Calcium and Vit D

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