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Diagnosis of Coeliac Disease

Learning objectives

By the end of this chapter, participants will be able to:

  • Describe the common symptoms of suspected coeliac disease (CD)
  • Recall the optimal tests for specific patient groups
  • Recount other useful tests to better diagnose and manage CD

Who should be tested for CD?

  • Patients with clinical symptoms associated with CD
  • Patients with conditions associated with an increased risk for CD
  • Patients with first-degree relatives with CD
  • History and symptoms that may be suggestive of CD are listed in the table below.1,2

Symptoms suggestive of CD - table

Why is CD difficult to diagnose?

  • CD can be difficult to diagnose because of the variety of clinical manifestations and overlap of symptoms with IBS.1
  • There is limited awareness for effective (or best practice) diagnostic approaches among healthcare professionals (HCPs) and patients in some regions.
  • Common myths surrounding CD may also contribute to misdiagnosis and poor diagnosis rates.1,3,5

Myths and Facts - table

Why should we test for CD?

  • It is estimated that there are approximately 4 undiagnosed cases of CD for every 1 diagnosed.6
  • Malabsorption due to CD results in damage to the small intestine mucosa with loss of absorptive surface area, reduction of luminal and pancreatic digestive enzymes with subsequent malabsorption of micronutrients, such as iron, vitamins and folic acid.2
  • Patients with long-term untreated CD have an elevated risk of developing lymphomas and some other malignant tumours, as well as infertility, bone issues and increased mortality from other complications of CD.1
  • For patients with symptomatic CD, introducing a GFD can lead to significant improvement in quality of life.1,5
  • Proactive case finding by screening for CD in high-risk groups, with a low threshold for serological testing, is considered the best approach for identifying patients with CD. Although CD meets several WHO criteria for mass screening, there is currently insufficient proof of its benefit, especially in people who are asymptomatic.1–3,5-7
  • There is an urgent need to increase awareness among physicians and paediatricians about the wide spectrum of CD’s clinical presentation and the pivotal role of serological testing in efficient CD diagnosis.1

Types of diagnostic methods

  • Before any investigations, it is crucial to ensure that the patient is ingesting gluten because all diagnostic tests (serology and biopsy) will be negative for CD on a gluten-free diet.7
  • Do not offer testing in infants before gluten has been introduced in the diet.2

Serology tests

  • Serology tests are based on immunoglobulin A (IgA) or immunoglobulin G (IgG). IgG-based tests are useful in selected IgA-deficient patients. Not one serological test has perfect sensitivity or specificity; therefore, serological tests may be combined to increase certainty of the result.3
  • Serological tests for CD1-3,7-8

• Serological tests for CD - table

  • Native gliadins: Antibody tests for native gliadins are no longer recommended for diagnostic purposes owing to their low sensitivity and specificity.1
  • Combinations of tests: The combination of serology tests that monitor different antigens, such as IgA-TG2 and IgG-DGP, may be useful.1 However, recent studies indicated that IgG-DGP positivity in the absence of IgA anti-TG2 may not be CD-specific.3

Histology and endoscopy


  • A combination of small intestine biopsy with a positive serological test is considered the gold standard test to confirm the diagnosis of CD.7
  • The villous atrophy may be patchy in CD; therefore, at least four biopsies of the distal duodenum and two biopsies of the bulb should be submitted for histological analysis.5,7
  • Duodenal biopsy changes in CD are typically graded by the Marsh classification (see Chapter 1).1
  • The most characteristic histological findings in patients with CD include:1
    • Increased density of intra-epithelial lymphocytes
    • Decreased villous-to-crypt ratio
    • Blunted or atrophic villi
    • Mononuclear cell infiltration into the lamina propria
    • Epithelial changes
  • The presence of only one of these changes raises the possibility of a different diagnosis.7
  • Histological changes in CD are distinctive, but not specifically indicative of CD as similar changes can also be observed with other infections and enteropathies (intestinal disease).1


  • Endoscopy is not sufficient to detect CD but some findings should raise suspicion of CD:1
    • Scalloping of duodenal folds
    • Fissuring over folds and a mosaic pattern in the mucosa
    • Flattening of folds
    • Decreased numbers of folds
    • Absence of villi
    • Granular appearance of the duodenal bulb
  • Endoscopic biopsies should be obtained from patients with duodenal abnormalities, or if CD is suspected and their endoscopic folds appear normal, as many patients have been shown to have apparently normal folds with confirmed CD.1
  • Among children with suspected CD who were DGP-positive but anti-TG2 negative, only 5% (8/148) had villous atrophy on biopsy.9
  • Video capsule endoscopy is recommended only for patients with positive CD serology who cannot undergo endoscopy with biopsy or when lesions or complications (ulcerative jejunitis) are suspected in the lower part of the intestines.3 This method cannot provide a tissue specimen for histology analysis. The sensitivity is restricted in the same way as conventional endoscopy, but the method is less invasive with good specificity.3

HLA genotyping

  • Human leukocyte antigen (HLA) testing alone is not sufficient for diagnosis.8,10
  • Testing negative for HLA-DQ2/DQ8 makes CD very unlikely.3
  • Approximately 30–40% of the general population also carry HLA-DQ2 and/or DQ8, without developing CD.10
  • The frequency of HLA-DQ2/DQ8 among first-degree relatives of patients with CD is generally higher than is seen in the general population (around 50–90%).11–13 The risk of developing CD for people carrying risk alleles is estimated to be between 36–53%.10
  • HLA tests may be used to exclude CD in patients already on a GFD or those with an idiopathic coeliac-like enteropathy.7
  • HLA tests can be useful for identifying high-risk subjects among those who have relatives with CD or those with specific genetic disorders.3
    • It can provide reassurance if negative and indicates monitoring or screening may be required if positive.3
    • There is evidence that almost 50% of newly diagnosed patients with CD within families are asymptomatic.1
    • DQ typing is less efficient for the estimation of CD risk in autoimmune diseases, which may themselves be linked to DQ2 or DQ8 even in the absence of CD.14–16

Skin immunofluorescence

  • Dermatitis herpetiformis (DH) is a common extraintestinal symptom of CD. Diagnosis of DH is confirmed by skin immunofluorescence to detect granular IgA deposition in the dermal papillae. A positive test is sufficient to prove CD in patients with DH regardless of serology and intestinal histology abnormalities.17

Diagnostic algorithm

Several different diagnostic methods are required to confirm a diagnosis of CD. Using only one method (from history, clinical examination, serology, human leukocyte antigen testing or histopathology) is not considered sufficient for diagnosis.18 Clinical assessment of CD alone is strongly discouraged since it is closely associated with misdiagnosis and can only help a minority of patients.1

Serology tests first

  • Anti-TG2 IgA and total serum IgA measurement are considered to be first-line tests for both symptomatic and asymptomatic CD.1
    • Negative anti-TG2 and normal total IgA is sufficient to exclude CD in patients with a low suspicion of CD.7
  • In children, high-titre anti-TG2 (≥10 x ULN) with positive EMA from a second blood sample are sufficient to confirm CD without a biopsy.18
    • The option for a no-biopsy diagnosis should be discussed with the patient’s family.18
    • Children with anti-TG2 positivity but ≤10 x ULN or with isolated DGP positivity should undergo intestinal biopsy to decrease risk of false positive diagnosis.18
    • DGP tests are not recommended for confirming CD in children with high anti-TG2 titres.18
  • In adults, a combination of a positive anti-TG2 or EMA serological test, together with villous abnormalities seen in intestinal biopsies, is currently the best diagnostic criterion for CD.1
    • The option to omit biopsy and rely on highly positive serology tests (as per paediatric guidelines) has been considered for adults but is not the ‘gold standard’ diagnostic criteria recommended by most guidelines.1–3,5,7
  • CD can be excluded in patients with negative anti-TG2/EMA with a negative HLA-DQ2/DQ8.1,3
    • Some HLA-DQ typing methods may not detect rare or variant DQ2 or DQ8 alleles in patients with positive anti-TG2/EMA18,19
  • A suggested diagnostic algorithm for serological testing is shown in Figure 1.

Serological Diagnostic Algorithm for Coeliac Disease. Adapted from Pelkowski & Vieara 2014

Figure 1: Serological Diagnostic Algorithm for Coeliac Disease. Adapted from Pelkowski & Vieara 2014.8

Confirming the diagnosis with histology

Marsh II/III

  • CD can be confirmed for patients with positive anti-TG2 antibodies and Marsh II or III lesions.3

Marsh I

  • Although Marsh I lesions (normal villous architecture and elevated intraepithelial lymphocytes) can be part of the histological spectrum of CD, only about 16% of cases with Marsh I have CD.3
  • Marsh I lesions can be seen in other enteropathies, food allergies, post-infectious conditions, etc., and may not be responsive to a GFD.3
  • Patients with dermatitis herpetiformis as the presenting symptom may have normal (Marsh 0) or Marsh I histology at the time of initial diagnosis. In such cases, a positive skin immunofluorescent test result can confirm the diagnosis (a routine skin histology test is not specific and not sufficient).17
  • In symptomatic patients and/or individuals with Marsh I classification and abnormal laboratory findings:
    • If anti-TG2 and EMA are positive, then CD is very likely; normal villous architecture with confirmed anti-TG2 and EMA positivity and correct HLA-DQ is called potential CD and requires a follow-up by a specialist3
    • If EMA is negative, an HLA test should be conducted. In the absence of HLA-DQ2/8, CD is excluded, while its presence does not provide any safe conclusion and another test should be performed after 6–12 months3
  • A diagnostic algorithm for patients with positive serology and Marsh I histology is shown in Figure 2.

Marsh 0 (normal histology)

  • In case of elevated anti-TG2 titre and normal histology report:
    • Biopsies should be assessed by a pathologist expert in CD, with special regard to how the biopsy sample was taken and the orientation of presentation.
    • Biopsy may be repeated after gluten challenge or longer follow-up on a gluten-containing diet.3
    • An HLA test and EMA should be performed.3
    • Presence of IgA deposits on transglutaminase in the gut tissues supports the diagnosis of CD, but this test is only conducted in specialised laboratories.20

Diagrams Positive serology

Figure 2: Suggested diagnostic approach for patients with positive serology and Marsh I histology. Adapted from Al-Toma A, et al. 2019.3

Optimal methods for diagnosis: The diagnostic cascade1

  • A universal “gold standard” diagnostic approach would require the epidemiology and clinical setting to be comparable worldwide, with diagnostic tests and medical treatment options widely available.
  • The World Gastroenterology Organisation (WGO) Global Guidelines Celiac Disease recommend diagnostic cascades, which provide resource-sensitive and context-sensitive options for diagnosis of CD.
  • A physician should always start with medical history taking and physical examination. Then, depending on the resource-sensitive options, the workflows described below should be followed.

Optimal methods for diagnosis: The diagnostic cascade - table

Adapted from WGO Global Guidelines Celiac Disease. 20161

Gluten challenge

  • Gluten challenge is a controlled diagnostic procedure under medical supervision and is useful when a final diagnosis of CD is questionable or previously insufficient in a person who is already using a GFD.5
  • A routine gluten challenge is no longer recommended for patients aged <2 years and fulfilling current diagnostic criteria of CD.
  • For a gluten challenge, a 14-day gluten intake at ≥3 g of gluten/day is recommended to provoke histological and serological changes in adult patients. The challenge may be prolonged to 8 weeks, depending on serology results.5
  • If an adult with undiagnosed CD is on a GFD, a gluten challenge of at least 3 months is recommended before elevated antibody levels appear, while in children diagnostic antibody levels may develop earlier or later.21,22
  • A GFD should be continued indefinitely, not only to prevent clinical relapse and malabsorption, but also to prevent complications.23 Although some research suggests that a certain proportion of patients may effectively develop tolerance to gluten, and thus become suitable for gluten reintroduction over time,23 past studies have indicated that histological relapse may occur even after several years on a gluten-containing diet, so long-term follow-up is needed.24

Differential diagnosis7

CD presents with similar signs and symptoms to other gastrointestinal complications, adding to the difficulty of recognizing and diagnosis of CD.  The table below summarises how these conditions can be differentiated from CD.

Differential diagnosis - table

Tests after diagnosis

  • Follow-up laboratory tests are recommended including full blood count, iron status (preferably ferritin), vitamin B12, vitamin D, calcium, and CD serology tests (preferably anti-TG2 or whichever serology test was initially positive).1
  • After the introduction of GFD, serological tests cannot detect minimal amounts of gluten intake therefore a multidisciplinary approach is needed to ensure mucosal healing and to encourage the patient’s adherence to a GFD.1 Persistently positive anti-TG2 or EMA tests indicates regular ingestion of significant quantities and non-adherence to a GFD by the patient.
  • Intestinal biopsies are essential for patients with persistent symptoms regardless of self-reported adherence to a GFD.1 If symptoms clear and serology test results return to normal, follow-up biopsies are not mandatory while on a GFD.
  • Liver enzyme abnormalities need to be monitored. If these abnormalities persist, further assessment (immunological, radiological, and/or histopathological) is needed.3
  • Additional duodenal biopsies may help evaluate mucosal healing and adherence to a GFD; however, recommended repetition timings are not well defined.1
  • Both adult and paediatric patients should be monitored annually for anthropometry, pubertal development and CD-specific serology. In addition, a bone mineral density scan should be conducted to evaluate changes in bone mass during a GFD.1 Testing for associated thyroid autoimmunity is also recommended (thyroid function, TSH, TPO).5
  • Serum intestinal fatty acid binding protein (I-FABP) measurement may be helpful in identifying persistent mucosal damage. Compliance to a GFD may also be assessed by the detection of gluten peptides from the stool or urine.3

Future developments

  • More specific diagnostic procedures, such as double-balloon enteroscopy, capsule endoscopy and magnetic resonance imaging may help in complicated cases.25
  • New techniques, such as confocal or high-resolution magnification endoscopy, optical band imaging and optimal coherence tomography may be more accurate and help to identify CD at an early stage, but there are cost, availability and tolerability issues associated with their use.5
  • When laboratory antibody assessments are not available, patient point-of-care rapid anti-TG2 tests can contribute to the initial assessment before any change in the gluten ingestion. Additionally, point-of-care tests can provide cost-effective alternatives to mass screening efforts for identification of undiagnosed CD cases.26-28


  • CD is difficult to diagnose due to the broad clinical spectrum of signs and symptoms and a lack of awareness for best diagnostic approaches among HCPs and patients.
  • Patients with long-term untreated CD have an increased risk of developing malignancies, fertility and bone issues, as well as an elevated mortality rate for other complications of CD.
  • Anti-TG2 IgA and total IgA tests are first-line tests to diagnose CD, for both symptomatic and asymptomatic CD.
  • If the first test is positive, or in case of borderline anti-TG2 IgA titres, additional immunoassays are recommended, such as EMA.
  • For IgA-deficient patients, the combination of IgG-DGP and anti-TG2 IgG (or IgG-EMA) is recommended.
  • HLA genotyping alone is not helpful in diagnosing CD but can be used to exclude CD in patients already on a GFD or those with a coeliac-like enteropathy.
  • An endoscopy or intestinal biopsies, together with a positive anti-TG2 or EMA serology test, are currently the best diagnostic criteria for CD.
  • Without serology results, histological lesions may not provide a specific/accurate diagnosis.
  • Children with a high (≥10 x ULN) anti-TG2 result and EMA positivity in a second blood sample, the final diagnosis of CD can be made without intestinal biopsies.
  • After diagnosis, serology tests should be performed including full blood count, iron status, vitamin B12, vitamin D, calcium and CD serology tests (e.g., anti-TG2 IgA).
  • Duodenal biopsies may also help to evaluate healing and adherence to a GFD.


  1. World Gastroenterology Organisation Global Guidelines. Celiac disease. 2016; Long Version: 1–35.
  2. NICE clinical guideline. Recognition and assessment of coeliac disease. 2015; [last accessed August 2020].
  3. Al-Toma A, Volta U, Auricchio R et al. European Society for the Study of Coeliac Disease (ESsCD) guideline for coeliac disease and other gluten-related disorders. United European Gastroenterol J. 2019;7(5):583–613.
  4. Vivas S, Vaquero L, Rodrigues-Martin L, Caminero A. Age-related differences in celiac disease: Specific characteristics of adult presentation. World J Gastrointest Pharmacol Ther. 2015;6(4):207–212.
  5. Ludvigsson JF, Bai JC, Biagi F, et al. Diagnosis and management of adult coeliac disease: guidelines from the British Society of Gastroenterology. Gut. 2014;63:1210–1228.
  6. Mustalahti K, Catassi C, Reunanen A, Fabiani E, Heier M, McMillan S, Murray L, Metzger MH, Gasparin M, Bravi E, Mäki M; Coeliac EU Cluster, Project Epidemiology. The prevalence of celiac disease in Europe: results of a centralized, international mass screening project. Ann Med. 2010 Dec;42(8):587-95
  7. BMJ Best Practice: Coeliac Disease. 2018. Available at: [last accessed November 2020].
  8. Pelkowski TD, Viera AJ. Celiac Disease: Diagnosis and Management. Am Fam Physician. 2014;89(2):99–105.
  9. Olen O, Gudjónsdóttir AH, Browaldh L, et al. Antibodies against deamidated gliadin peptides and tissue transglutaminase for diagnosis of pediatric celiac disease. J Pediatr Gastroenterol Nutr. 2012;55(6):695–700.
  10. Sciurti M, Fornaroli F, Gaiani F, et al. Genetic susceptibility and celiac disease: what role do HLA haplotypes play? Acta Biomed. 2018;89(Suppl 9):17–21.
  11. Özgenel S, Temel T, Teke H, et al. HLA-DQ2/DQ8 frequency in adult patients with celiac disease, their first-degree relatives, and normal population in Turkey. Turk J Gastroenterol. 2019;30(4):321–325.
  12. Castro-Antunes MM, Crovella S, Brandao LAC, et al. Frequency distribution of HLA DQ2 and DQ8 in celiac patients and first-degree relatives in Recife, northeastern Brazil. Clinics. 2011;66(2):227–231.
  13. Cecilio LA, Bonatto MW. The prevalence of HLA DQ2 and DQ8 in patients with celiac disease, in family and in general population. Arq Bras Cir Dig. 2015;28(3):183–185.
  14. Regnell SE, Lernmark Å. Early prediction of autoimmune (type 1) diabetes. Diabetologia. 2017;60(8):1370–1381.
  15. Mohammadi J, Pourpak Z, Jarefors S, et al. Human leukocyte antigens (HLA) associated with selective IgA deficiency in Iran and Sweden. Iran J Allergy Asthma Immunol. 2008;7(4):209–214.
  16. Korponay-Szabó IR, Dahlbom I, Laurila K, et al. Elevation of IgG antibodies against tissue transglutaminase as a diagnostic tool for coeliac disease in selective IgA deficiency. Gut. 2003;52(11):1567–1571.
  17. Reunala T, Salmi TT, Hervonon K, et al. Dermatitis Herpetiformis: A common extraintestinal manifestation of coeliac disease. Nutrients. 2018;10(5):602.
  18. Husby S, Koletzko S, Korponay-Szabo I, et al. ESPGHAN Guidelines for diagnosing Coeliac Disease. J Pediatr Gastroenterol Nutr. 2020;70(1):141–157.
  19. Werkstetter KJ, Korponay-Szabó IR, Popp A, et al. Accuracy in diagnosis of celiac disease without biopsies in clinical practice. Gastroenterology. 2017;153(4):924–935.
  20. Taavela J, Popp A, Korponay-Szabo IR, et al. A prospective study on the usefulness of duodenal bulb biopsies in celiac disease diagnosis in children: urging caution. Am J Gastroenterol. 2016;111(1):124–133.
  21. Korponay-Szabó IR, Kovács JB, Lörincz M, et al. Prospective significance of antiendomysium antibody positivity in subsequently verified celiac disease. J Pediatr Gastroenterol Nutr. 1997;25(1):56–63.
  22. Hellman R. Gluten Free Diets – A Challenge for the Practicing Physician. Mo Med. 2020;117(2):119–123.
  23. Itzlinger A, Branchi F, Elli L, et al. Gluten-Free Diet in Celiac Disease-Forever and for All? Nutrients. 2018;10(11):1796.
  24. Högberg L, Stenhammar L, Wågermark J. Very late mucosal relapse in a girl with coeliac disease. Acta Paediatr. 1993;82(10):887–889.
  25. Fasano A, Catassi C. Clinical practice. Celiac disease. New Engl J Med. 2012;367(25):2419–2426.
  26. Pasinszki T, Krebsz M. Advances in celiac disease testing. Advances in Clinical Chemistry. 2019; Volumne 91; 1-29.
  27. Esteve M et al. Case-finding in primary care for coeliac disease: Accuracy and cost-effectiveness of a rapid point-of-care test. UEG Journal. 2018; 6(6) 855-865.
  28. Korponay-Szabo IR, Raivio T, Laurila K, Opre J, Kiraly R, Kovacs JB, Kaukinen K, Fesus L, Maki M. Coeliac disease case finding and diet monitoring by point-of-care testing. Aliment Pharmacol Ther. 2005; 22: 729-737.
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