Upper Endoscopy with Biopsy is something that seems to cause a great deal of debate in the online Celiac community. Every day I see posts where people say their blood test was positive, but they don’t want to have the endoscopy. Or their blood test was negative and they want to have the biopsy just to confirm the blood test was right.

Note: Those with a confirmed biopsy of Dermatitis Herpitformis (Celiac skin rash) this does not apply to you. You have DH and have to have a gluten free diet for the rest of your life. Congrats!! This does not apply to you!

What is endoscopy like?

The diagnostic procedure for visual inspection of the esophagus, stomach, and duodenum is called
Esophagogastroduodenoscopy. It can be performed with and without biopsy. For the purposes of this article, I’m going to call the
Esophagogastroduodenoscopy with biopsy – an Endoscopy.

Preparation for the procedure by the patient is typically consuming nothing by mouth after midnight the night before the procedure. Normally, the patient is given a mouth guard to protect the teeth from the endoscope (tool that is inserted into the body). A “twilight” anesthesia is given – basically asleep but not a deep sleep.

The endoscope is passed through the mouth, esophagus, stomach, and first and second parts of the duodenum (small intestine). Still pictures can be taken during the procedure. A visual examination is done of the esophagus, stomach, and duodenum. Samples are taken of each part visually reviewed and prepared for the pathologist to review.

The entire procedure takes about 10 minutes to complete. Normally, there is no lingering pain, but the patient may have some gas that needs to be expelled – lots of burping – after. Pretty simple stuff, right?

Some people have fears about anesthesia, pain, or damage to their internal organs. These are all valid fears and should be discussed with their doctor before undergoing any procedure.

Why biopsy?

Celiac disease is defined by blunted villi and increased intraepithelial lymphocytes in the small intestine. These can only be visualized via endoscopy. The blood tests indirectly measures the body’s immune response to gluten. (I’ll get into the details of the blood tests and what they measure in another post.) The blood tests do not correlate to damage in the small intestine. A person could be just barely positive and have completely destroyed villi or a person could have highly positive numbers and just barely destroyed villi. They do not correlate. The only thing the blood tests indicate is that the immune system is reacting to something.

Also, damage to the intestine is graded on the Marsh scale. Marsh 0 and 1 do not indicate Celiac disease. They don’t indicate “early” damage either. People saying this are not accurate. Marsh 1 damage can be caused by something as simple as taking acetomiphen or naproxen sodium within a week or two of the test or SIBO or H. Pylori. If Marsh 1 damage is found, this is not indicative of active Celiac disease.

Marsh 2 damage is unusual and typically only seen with Dermatitis Herpitformis. Marsh 3 and above damage is definitive Celiac damage – no ifs, ands, or buts.

False positive/negatives on blood tests

When performing any blood test for the diagnosis of Celiac disease, the patient must be consuming gluten for at least 6 weeks prior to the test. Consuming gluten means at least 2 slices of bread or equivalent. Deviation from standard means the test improperly administered and does not make the test inaccurate.

These blood tests are not accurate on children under 2, please consult your pediatric gastroenterologist for more.

The tTG- IgA is the test most often used today to determine Celiac disease. When performed correctly it is highly accurate and specific. According to a comparative analysis of Celiac blood tests the test is approximately 92% (lowest average) accurate and 97% specific. There are additional tests that can be done. EmA-IgA is 75% accurate, but more than 80% specific and some even say 100% specific. The DGP IgA is about 90% accurate and 90% specific.

But note, the EmA-IgA and DGP IgA tests when combined with biopsy were only 80% accurate for the patient to get the final Celiac diagnosis. They did not look at tTg-IgA.

All really good tests. They should give a strong suspicion of Celiac disease if one or multiple of these tests are done accurately. But 20% of the time these blood tests when combined biopsy did not yield a diagnosis of Celiac.

But there are some exceptions. Other diseases can cause these tests to register falsely positive or negative. False results can be caused by thyroid disease, liver disease, H. pylori infection, tropical sprue, other autoimmune diseases, IgA deficiency, and congestive heart failure.

Also, note that the Amercian Academy of Gastroenterology says that if a person’s tTG-IgA is over 10x the upper limit, then a diagnosis of Celiac disease can be made by blood test alone. So, if positive tTG IgA starts at 20 and your test result is 200, there is no need to move to an endoscopy. You get to eat gluten free for the rest of your life!

So, really, if any of the blood tests are positive it is time to move to the biopsy phase of diagnosis. If any test is negative, personally, I would stop here and if still experiencing issues retest in 6 months. A blood test is a lot easier than an endoscopy.

To Biopsy or Not

I’ve laid out that the blood test can be inaccurate 20% of the time, the biopsy is an easy procedure, and Celiac has a specific definition of blunted villi and increased intraepethelial lympocytes – why wouldn’t you? Here’s more reasons to have the biopsy.

Every medical journal and diagnostic guideline requires it. The criteria to enter drug trials for Celiac drugs require a positive biopsy to move forward. 504 plans for school require it. Court orders to make your divorced spouse feed your children gluten free foods require it. FMLA requires it. Every single piece of documentation for any special accommodations or needs requires a definitive diagnosis. Your diagnosis will be indefensible in court if you don’t have the biopsy.

A frustrating scenario would be where the blood tests are positive and the biopsy is negative. This puts you in a bit of limbo and requires you and your doctor to do some more work. In this scenario, it is recommended to continue a gluten-filled diet and retest in 3-6 months. The blood test could have been done wrong, there could have been a problem with the sample, or any number of things could have gone wrong.

A bad case scenario is where the doctor that diagnosed you retires, closes their practice, or just gets run over by a bus (I don’t hope this happens, its just demonstrating something random that can happen.). All medical records are lost or you simply have to change doctors. The new doctor looks at your records and says, “Nope, I don’t think you have Celiac, you are missing biopsy results. Please do a gluten challenge so that we can diagnose you properly.” Now, you are in the gluten challenge and because you’ve been gluten free for so long, and that it is miserable.

A worse case scenario is what if you are the 20% of people where the biopsy would indicate there is no Celiac. You’ve been gluten free for NOTHING? I cannot imagine how frustrated I would be if I was living gluten free under the assumption that I had Celiac only to find out later it was a big waste of time. Ugh!

Here’s the final reason – because it is required for a complete diagnosis.

Personal Note

Upon initial diagnosis for me, I did not get the biopsy. All of my blood tests tTG-IgA, DGP-IgA, and EMA-IgA were all at least 10x the positive marker. A year after diagnosis and being gluten free, I had the endoscopy. My blood tests had dropped significantly, but were not normal, yet. I had a Marsh 3C designation after a year of being gluten free. So, the idea that doctors can’t find damage to me seems unrealistic. But some people have patchy damage and it is possible.


I know I’m going to get some push back on this. Some will say a endoscopy is not necessary, they know they have Celiac. Okay. If you and your doctor made that decision, I’m a stranger on the internet and don’t know anything about your life. You decided.

At the same time, there are lots of people out there that need to hear scientifically proven and accurate information. Current standards for diagnosis require endoscopic biopsies with proven damage to the small intestine. This is factually accurate with the caveats I listed in the article. If deviation from the standard is what you decide, then okay. But at least know and understand the standard procedures. That is what I’m trying to explain here.

I know this is scary – especially for the kids. But just do it. It makes you 100% certain you have Celiac. It gives you a baseline to determine healing when the repeat endoscopy is completed in 2 years. It makes the diagnosis real when if you don’t, you will always question the diagnosis.

For those that have already forgone the endoscopy, I would suggest you get one now. Yesterday cannot be altered, but moving forward you will know where you stand.

I’m not a doctor, nor do I pretend to be one. Take all of my suggestions and advice with a grain of salt. This is my blog and my opinion. Research all of what I say and call me out if I’m wrong. Discuss this with your doctor and make the best choices for your unique situation.

6 responses to “To Endoscopy or Not – That is the Question”

  1. Susan Avatar

    Thanks for the info on DH. I’m positive that I have it but cannot find a dermatologist that knows how to do the biopsy correctly. I read the research & the biopsy is not at all a normal way of doing a biopsy. I’ll keep trying to find a savvy MD to do it but until then it’s difficult to find out anything about DH & if it’s definitely a sign of celiac. I think you are saying, yes, it is.

    1. Corinne Avatar

      I agree with you completely. No symptoms but have osteoporosis. Confirmed celiac on endoscopy because of an excellent endocrinologist.

    2. Marisa Avatar

      I had a negative celiac panel, should I wait to test again before going ahead with an endoscopy?

      1. FatCeliac Avatar

        I would say that if your celiac panel is negative and they did the right celiac tests, then there really isn’t much point in an endoscopy. When done correctly, the celiac tests are specific and accurate. When done incorrectly or misinterpreted, they are useless. So, talk to your doctor and make sure you are comfortable with the decision to not proceed with an endoscopy at this time.

  2. Martha Shields Avatar
    Martha Shields

    Ok, so you laid out why an endoscopy is necessary for a solid diagnosis… but you did not convince me on WHY you need a solid diagnosis in tHe first place. This is a disease with no treatment but for a gluten free lifestyle – if you are told you are Celiac based on blood tests and symptoms, and you feel and function better on a gluten free diet, then stick with it, diagnosis or not. I have never been able to find, for US residents, any legal or financial reason to be diagnosed with an endoscopy/biopsy. And even if there were, like maybe for job qualifications or a student’s 504 plan, a doctor’s note would suffice when your doctor is willing to diagnose you with symptoms and a positive blood test.

    1. FatCeliac Avatar

      I will lay out that argument on Monday. It is a fair question and more complex than just a quick answer I have time for today. But the first answer is for follow up care and why that is important. The second answer is that just because this doctor says you have it doesn’t mean the next doctor will. The third answer is that I believe that medicines will soon be available to help. The fourth answer is that most people feel better on a gluten free diet because it cuts out a lot of junk and rhat doesnt necessarily mean celiac disease. The fifth answer is what if your issues are more serious and simply cutting gluten masks them. That’s just off the top of my head for now. You will see more Monday.

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