Villous atrophy occurs when your intestinalvilli—the microscopic, finger-like tentacles that line the wall of your small intestine—erode away, leaving a virtually flat surface.
Since your intestinal villi are responsible for absorbing the nutrients contained in the food you eat, losing them to villous atrophy can result in serious nutritional deficiencies.

In the worst-case scenario with celiac disease, your villi can be completely destroyed — total villous atrophy. That’s considered Marsh Score 4, and people with that score are likely to be severely malnourished and may be at risk for lymphoma.
The only way to see if you have villous atrophy is to look directly inside your small intestine.
Healthcare providers do this with a procedure called anendoscopy, in which they thread a device with a tiny camera and other instruments down your throat, through your stomach, and into your small intestine. It’s also possible to swallow a pill containing a camera—this is calledcapsule endoscopy.
However, the advantage of doing endoscopy is to be able to sample the small bowel ( take biopsy) to confirm diagnosis of celiac disease, whereas capsule endoscopy only helps visualization of the small bowel but biopsies can not be taken.
Villous Atrophy and Celiac Disease
You’re not guaranteed to have celiac disease just because you have villous atrophy. Several other conditions, plus some medications and even bacterial overgrowth, can destroy your intestinal villi.
Therefore, it can be tricky to tell the difference between celiac disease and nonceliac enteropathy. That’s why healthcare providers recommendceliac disease blood testing—those tests look for your immune system’s specific reaction to the gluten protein in the foods you’re eating.
It’s still possible to have celiac disease even with negative results on those blood tests, but if you don’t start to feel better once you go gluten-free, you and your healthcare provider may need to consider alternative causes for your symptoms and your villous atrophy.
Other Causes of Villous Atrophy
Here’s a list of some possible alternate causes of villous atrophy:
Other possible causes of villous atrophy, including infection with parasites (giardia), bacteria (Whipple disease), mycobateria (tuberculosis) or other autoimmune conditions like autoimmune enteropathy also have been reported.
5 SourcesVerywell Health uses only high-quality sources, including peer-reviewed studies, to support the facts within our articles. Read oureditorial processto learn more about how we fact-check and keep our content accurate, reliable, and trustworthy.Martins C, Teixeira C, Ribeiro S, et al.Seronegative Intestinal Villous Atrophy: A Diagnostic Challenge.Case Rep Gastrointest Med. 2016;2016:6392028. doi:10.1155/2016/6392028Wierdsma NJ, Van bokhorst-de van der schueren MA, Berkenpas M, Mulder CJ, Van bodegraven AA.Vitamin and mineral deficiencies are highly prevalent in newly diagnosed celiac disease patients.Nutrients. 2013;5(10):3975-92. doi:10.3390/nu5103975Tam JS, Routes JM.Common variable immunodeficiency.Am J Rhinol Allergy. 2013;27(4):260–265. doi:10.2500/ajra.2013.27.3899Ha F, Khalil H.Crohn’s disease: a clinical update.Therap Adv Gastroenterol. 2015;8(6):352–359. doi:10.1177/1756283X15592585Küppers R, Engert A, Hansmann ML.Hodgkin lymphoma.J Clin Invest. 2012;122(10):3439–3447. doi:10.1172/JCI61245Additional ReadingDeGaetani M et al. Villous atrophy and negative celiac serology: a diagnostic and therapeutic dilemma.American Journal of Gastroenterology. 2013 May;108(5):647-53.Pallav K et al. Noncoeliac Enteropathy: The Differential Diagnosis of Villous Atrophy in Contemporary Clinical Practice.Alimentary Pharmacology & Therapeutics. 2012;35(3):380-390.Tran TH et al. Olmesartan and Drug-Induced EnteropathyPharmacy and Therapeutics. 2014 Jan; 39(1): 47–50.
5 Sources
Verywell Health uses only high-quality sources, including peer-reviewed studies, to support the facts within our articles. Read oureditorial processto learn more about how we fact-check and keep our content accurate, reliable, and trustworthy.Martins C, Teixeira C, Ribeiro S, et al.Seronegative Intestinal Villous Atrophy: A Diagnostic Challenge.Case Rep Gastrointest Med. 2016;2016:6392028. doi:10.1155/2016/6392028Wierdsma NJ, Van bokhorst-de van der schueren MA, Berkenpas M, Mulder CJ, Van bodegraven AA.Vitamin and mineral deficiencies are highly prevalent in newly diagnosed celiac disease patients.Nutrients. 2013;5(10):3975-92. doi:10.3390/nu5103975Tam JS, Routes JM.Common variable immunodeficiency.Am J Rhinol Allergy. 2013;27(4):260–265. doi:10.2500/ajra.2013.27.3899Ha F, Khalil H.Crohn’s disease: a clinical update.Therap Adv Gastroenterol. 2015;8(6):352–359. doi:10.1177/1756283X15592585Küppers R, Engert A, Hansmann ML.Hodgkin lymphoma.J Clin Invest. 2012;122(10):3439–3447. doi:10.1172/JCI61245Additional ReadingDeGaetani M et al. Villous atrophy and negative celiac serology: a diagnostic and therapeutic dilemma.American Journal of Gastroenterology. 2013 May;108(5):647-53.Pallav K et al. Noncoeliac Enteropathy: The Differential Diagnosis of Villous Atrophy in Contemporary Clinical Practice.Alimentary Pharmacology & Therapeutics. 2012;35(3):380-390.Tran TH et al. Olmesartan and Drug-Induced EnteropathyPharmacy and Therapeutics. 2014 Jan; 39(1): 47–50.
Verywell Health uses only high-quality sources, including peer-reviewed studies, to support the facts within our articles. Read oureditorial processto learn more about how we fact-check and keep our content accurate, reliable, and trustworthy.
Martins C, Teixeira C, Ribeiro S, et al.Seronegative Intestinal Villous Atrophy: A Diagnostic Challenge.Case Rep Gastrointest Med. 2016;2016:6392028. doi:10.1155/2016/6392028Wierdsma NJ, Van bokhorst-de van der schueren MA, Berkenpas M, Mulder CJ, Van bodegraven AA.Vitamin and mineral deficiencies are highly prevalent in newly diagnosed celiac disease patients.Nutrients. 2013;5(10):3975-92. doi:10.3390/nu5103975Tam JS, Routes JM.Common variable immunodeficiency.Am J Rhinol Allergy. 2013;27(4):260–265. doi:10.2500/ajra.2013.27.3899Ha F, Khalil H.Crohn’s disease: a clinical update.Therap Adv Gastroenterol. 2015;8(6):352–359. doi:10.1177/1756283X15592585Küppers R, Engert A, Hansmann ML.Hodgkin lymphoma.J Clin Invest. 2012;122(10):3439–3447. doi:10.1172/JCI61245
Martins C, Teixeira C, Ribeiro S, et al.Seronegative Intestinal Villous Atrophy: A Diagnostic Challenge.Case Rep Gastrointest Med. 2016;2016:6392028. doi:10.1155/2016/6392028
Wierdsma NJ, Van bokhorst-de van der schueren MA, Berkenpas M, Mulder CJ, Van bodegraven AA.Vitamin and mineral deficiencies are highly prevalent in newly diagnosed celiac disease patients.Nutrients. 2013;5(10):3975-92. doi:10.3390/nu5103975
Tam JS, Routes JM.Common variable immunodeficiency.Am J Rhinol Allergy. 2013;27(4):260–265. doi:10.2500/ajra.2013.27.3899
Ha F, Khalil H.Crohn’s disease: a clinical update.Therap Adv Gastroenterol. 2015;8(6):352–359. doi:10.1177/1756283X15592585
Küppers R, Engert A, Hansmann ML.Hodgkin lymphoma.J Clin Invest. 2012;122(10):3439–3447. doi:10.1172/JCI61245
DeGaetani M et al. Villous atrophy and negative celiac serology: a diagnostic and therapeutic dilemma.American Journal of Gastroenterology. 2013 May;108(5):647-53.Pallav K et al. Noncoeliac Enteropathy: The Differential Diagnosis of Villous Atrophy in Contemporary Clinical Practice.Alimentary Pharmacology & Therapeutics. 2012;35(3):380-390.Tran TH et al. Olmesartan and Drug-Induced EnteropathyPharmacy and Therapeutics. 2014 Jan; 39(1): 47–50.
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