The Intestinal Villous Blunting (Flattening) in Celiac Disease is often “Patchy”

Villi are the fingerlike projections of the small intestine where nutrient absorption takes place and are the location of Celiac Disease’s assault on the digestive tract.

Untreated celiac disease leads to blunting (flattening) of the intestinal villi that can be seen when a gastroenterologist performs an endoscopy with biopsy. Despite current controversy over whether or not an endoscopy is necessary for all cases of celiac diagnosis, it is still considered by many experts to be the “gold standard” for officially diagnosing Celiac Disease. I look forward to learning more about this moving target at the International Celiac Disease Symposium being hosted by the University of Chicago in September 2013 (see link).

Although in many cases of Celiac Disease the villous blunting is continuous throughout the small intestine, it has been increasingly recognized that the blunting/flattening can be patchy, and in some cases, localized to one specific portion of the small intestine called the duodenal bulb (see references). Thus, in many cases of Celiac Disease, totally normal areas of intestine alternate with diseased areas. Because of this, experts recommend that gastroenterologists take at least 3 to 4 biopsies, including at least one of the duodenal bulb, when evaluating a patient for Celiac Disease. If not enough biopsies are taken, the diseased portions of the small intestine may be missed (and hence, Celiac Disease not properly recognized). Since starting this blog last fall I have interacted with many people who get terribly ill from eating gluten, have many symptoms of Celiac Disease and have abnormal Celiac antibodies on blood testing, only to be told that they do not have Celiac Disease based on “normal” biopsies. I have also encountered one woman in which no biopsies were taken at all! I strongly suspect that some of these “gluten intolerant” people actually have Celiac Disease.

A group of researchers in Italy (Valitutti, et al.) have recently published the findings of a study in which they mapped the patchiness of villous blunting in 41 pediatric patients with Celiac Disease. 17/41 (41.5%) showed diffuse villous blunting throughout and 24/41 (58.5%) had patchy villous lesions. Of note, one child with Celiac Disease had villous blunting in the jejunum, the second portion of the small intestine, only. In most cases only the duodenum, the first portion of the small intestine, is biopsied, so had this child not had his jejunum biopsied for the study, his celiac changes would have been missed. I find this to be very significant, as he would have likely been labeled as being gluten intolerant, or having “Potential” Celiac Disease as opposed to having actual Celiac Disease….for more on Potential Celiac Disease, please see my previous post from March 2013.

In conclusion, if you are one of the gluten intolerant or gluten sensitive patients out there who had a “normal” biopsy (or are parents of one), I encourage you to obtain your biopsy results and check out how many tissue samples were actually taken from your small intestines. Check also to see if your duodenal bulb was evaluated. You may be surprised by what you find!

Also, if you are going to be attending the Celiac Disease Symposium in Chicago next month I would love to connect with you in person. Shoot me an email at, or comment below. We are very fortunate to be having it be held in the U.S.A. this year and it will be a great opportunity to learn and network.


1. Valitutti, F., et al. Mapping histologic patchiness of celiac disease by push enteroscopy. Gastrointestinal endoscopy. E-pub, ahead of print. June 2013.

2. Kurien, M., et al. Duodenal bulb biopsies for diagnosing adult celiac disease: is there an optimal biopsy site? Gastrointestinal Endoscopy. 2012. 75 (6): 1190-6.

3. Ravelli, A., et al. How patchy is patchy villous atrophy?: distribution of histological lesions in the duodenum of children with celiac disease. American Journal of Gastroenterology. 2010. 105(9): 2103-10.

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17 thoughts on “The Intestinal Villous Blunting (Flattening) in Celiac Disease is often “Patchy”

  1. Gayle Weber

    I just wanted to thank you for your research and blogging about celiac. I am gluten intolerant with multiple food sensitivities. I have an IgG reaction to gluten and wheat, as well as rye and barley and numerous other things. Since removing gluten, dairy and soy from my diet, I have noticed a great improvement in my digestive health but conversely, when gluten or other offenders are accidentally ingested, my reaction is much more severe than it was before I removed them from my diet. I understand the conventional wisdom indicates getting all the necessary tests for celiac before going off gluten but I have only gotten the food allergy testing done (IgG & IgE). Are there any tests developing which can diagnose celiac retroactively after removing gluten from the diet? I am also concerned that my 18 year old daughter may have it. She has not removed gluten from her diet but has many of the symptoms. Your thoughts are appreciated.

    1. Jess Post author

      Hi Gayle,
      You have great questions. As far as I know, there are no tests that can diagnose Celiac Disease after going GF, outside of putting yourself through a “gluten challenge” which consists of eating between 1/2 to 1 slice of bread for 2-4 weeks (depending on the source) and then having Celiac antibodies drawn and undergoing an endoscopy with biopsy. I know that there are some tests in the works right now, but we are years and years away from this. I am unable to speak to the tests available by alternative labs and practitioners, as I have been keeping up to to date with traditional medicine for the most part.
      Since you are gluten intolerant/possibly Celiac, I would strongly recommend that your daughter get tested for Celiac Disease while she is still on a gluten containing diet. There has been a recently published paper that shows that untreated Celiac Disease is associated with lymphoma, a type of cancer, so I am encouraging anyone with symptoms and/or a family history of Celiac/gluten intolerance to get tested to prevent the development of cancer. The link to this paper is in my most recent post.
      I wish the best to you. Please let me know if you have any further questions.

  2. Pingback: Updates on Celiac Disease Screening and Testing from the 2013 International Celiac Disease Symposium | The Patient Celiac

  3. Robyn Lucas

    Hi Jess
    I just wanted to thank you for setting up this website. I found it really helpful. I am in the process of determining if I have Celiacs. I have patchy damage to my gut as well as the gene so now have to do the gluten elimination diet. I just wanted your thoughts as to our son. He has had very low iron for some time and had an endoscopy that showed damage to his oesophagus and minor changes in his duodenum (slightly blunted villi). At the time I didn’t know about me and since he has had the gene test for celiac and it is negative. Should he get tested again ie can you get a false negative genetic test ?? Does he need another endoscopy.
    Kind Regards

    1. Jess Post author

      Hi Robyn,
      Thanks for stopping by and for your kind words.
      It sounds to me like you have celiac disease if you have small intestinal damage, symptoms, and one of the main genes. I hope that the diet is going well for you and that you are feeling better
      Depending on the source, between 95 and 99% of celiacs have one of the main 2 celiac genes (HLA-DQ2 or DQ8). I am proof that you can have celiac disease without one of the main genes though. I am DQ7 positive, and this gene has been associated with celiac in other parts of the world, including Italy (I am Sicilian). With your history, and your son’s anemia and abnormal initial biopsy I’d be concerned that he’s somewhere on the celiac disease spectrum. There was actually a poster of an abstract presented at the International Celiac Disease Synposium in September that showed that 9% of Brazilans with celiac disease are DQ2/DQ8 negative as well. Just some food for thought…If he’s still on a regular diet containing gluten it may be a good idea to have the scope repeated and to see what is going on with his villi (and his esophagus).

  4. Pingback: “Gluten intolerance” can actually be subclinical celiac disease | The Patient Celiac

  5. Jason

    I had biopsies that showed mild villous blunting in the small intestine. I had symptoms like stomach gurgling, bloating, nausea, and either large soft stools or diarrhea. It will flare up for a few weeks and disappear for months. I had blood results all negative for celiac disease. My Gastroenterologist says I don’t have celiac disease. Is there something else that can cause the villous blunting like a food allergy? Thanks for your time.

    1. Jess Post author

      Hi Jason,
      I just wrote about the other causes of villous blunting in my latest post, the link is here. Were you already on the GF diet when your blood tests were done? I ask because this can cause a false negative result.
      It may also be possible that you have seronegative celiac disease (normal celiac antibodies but biopsy that is abnormal).
      Are you feeling better on the GF diet?

  6. Julie Wilson


    I was very happy to find your blog and this article in particular. I wanted to ask your opinion, and I apologize in advance for the long note. I have had constant and painful GI symptoms for my whole life, as well as infertility and autoimmune thyroid disease. I used to see a GI doctor when I was in my 20s (I am now 40) and he never seemed to take me seriously. After a few years of fruitless office visits, he did an endoscopy that showed blunting of the duodenal folds and abnormal mucosa (I actually have a hard copy of the endoscopy report). He suspected celiac but then said the biopsy came back negative.

    Fast forward 15 years or so, and both of my daughters are diagnosed with celiac disease at ages 4 and 6. I was still having the same symptoms I had always had and was on thyroid meds, reflux meds and metformin for my fertility issues, as well as some antispasmodic I can’t remember the name of. My daughters’ GI doctor suggested my husband and I get tested for celiac (I actually showed him my own endoscopy report and he said “That is celiac.”). I returned to my old GI doctor after nearly a decade. He was not interested in looking at my old biopsy and he didn’t really think the visit was necessary, but at my urging he ran a blood test for celiac that came back normal

    Because my daughters were upset with their celiac diagnosis, my husband and I decided to go gluten free (our whole house) out of solidarity. I stopped taking my metformin and thyroid pills and the others at the same time as a little test because I suspected I might also have celiac despite my test results. Within a few weeks on the diet, my stomach/digestive issues were gone and I started my period on my own (which I had not done in more than a decade without a prescription). My thyroid also has tested normal for its function every time I get a blood test (on a strict GF diet).

    I apologize for the long way around to my question, but I wanted to give you the back story. Do you think it is worth pursuing celiac testing? If my problems were indeed caused by celiac, I would love to have an official diagnosis. However, after years of not having my doctor treat me seriously (and frankly disregard me as a hypochondriac), I avoid seeing the doctor. In fact, I really hate going and am a terrible advocate for myself because I am afraid of being treated the same way by a new doctor. Also, I remember how bad I felt when I ate gluten, and I really would like to not eat it and feel that way again.

    I feel great on the GF diet, and it seems to me that it would be easy just to stay on it forever. Is it better to just stick to a strict GF diet, or is there any benefit to knowing conclusively if it is celiac?

    Thank you for any insight you can provide.



    1. Jess Post author


      With all of your lifelong symptoms, your intestines with blunting in your twenties, and 2 children with celiac disease I would have to guess that you are also a celiac. I hate to be blunt but it sounds like your GI doctor probably dropped the ball on your diagnosis and did not take enough biopsy samples…this is one of the most common causes of celiac diagnoses being missed.

      I encourage most people to get tested for celiac so that they can find out whether or not their children and other relatives are at risk, but in your case you already know this is the case since your daughters have it.

      I am not allowed to give true medical advice on here, but if I were you I would believe your daughters’ GI physicians assessment that you have celiac disease…it also sounds like it would explain all of your symptoms and medical problems (and explain why you feel so much better on the GF diet).

      I hope this helps.


      P.S. Please fire your gastroenterologist!!!

      1. Julie Wilson


        Thank you! Ha! I promise never to see the old GI doc again. That promise will be easy to keep.

        I guess since I feel great and just need to stick to the diet our entire family already is doing, then I will just carry on.

        I appreciate your response! Take care,


  7. Dawn

    i am wondering why I still have Vilnius atrophy every time I have an endoscopy? I am on a strict gf diet and no dr has explained this to me.

  8. Dawn

    I am wondering why I continue to have villous atrophy after a really strict gf diet? No doctors have addressed this with me and I continue to have intestinal issues. I have chronic chest pain (atypical) and nobody knows why. Really wishing for some relief. Please share any thoughts you might have with me.

    Thank you,

    1. Jess Post author

      Hi Dawn,
      Thank you for writing.
      The most common cause of persistent symptoms in those of us with celiac is unintentional/accidental gluten exposure. Are your celiac antibodies still elevated in your blood?
      It can take a few years for total healing of the villi. When did you have your last scope dine and how long have you been GF?
      If you’ve been GF for 6 to 12 months, and know that you still have villus blunting, you should probably be seen at a center that specializes in celiac disease, if possible.
      Hope you are able to get some answers.

  9. Jacqui

    Sorry for the long story, just want you to get the full picture. My son is 16 years old. He has always had bad eczema all his life. This past year he started vomitting when he was eating, he would say it felt like something in his throat and then he would throw up. This could happen a few times a week then nothing for a month. He lost 30 pounds in a short period of time not even trying. His regular dr didn’t think it was anything as he was at his normal weight. I went to a ENT to make sure it was not his tonsils or an obstruction which it was not. I decided to take him to a gastro who did an endoscopy. They found villous atrophy in the duedonal bulb and normal villous architecture in the small intestines. The gastro dr now wants to do bloodwork because he is not sure if its celiac disease or not. Does this sound like celiac to you?
    Thank you for your imput on this!

    1. Jess Post author

      Hi Jacqui,
      While I canont give your son a diagnosis, I can say that yes, the damage from celiac (villous atrophy) can be confined to the duodenal bulb only–this is one of the reasons that celiac can be missed on biopsy (if the bulb is not sampled). You may want to consider a second opinion, and/or get him seen at a academic center that has a dedicated celiac disease center.
      I hope that your son starts to feel better soon.

      1. Jacqui

        Thank you so much for your response! I am waiting for results from his bloodwork and will see what that brings I may need a second opinion fro
        A celiac specialist especially since he also has a bad rash thank you again!

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