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Surgical Pathology Criteria

Autoimmune Enteropathy


Alternate / Historical Names

  • Generalized autoimmune gut disorder

See also

  • IPEX syndrome(Immune Dysregulation, Polyendocrinopathy, Autoimmune Enteropathy, X-linked)

Diagnostic Criteria

  • Autoimmune enteritis usually presents in first six months of life
  • Principally involves small intestine
    • May also involve stomach and large intestine
  • Nearly all show partial or complete villous atrophy
  • Nearly all show an increase in lamina propria lymphocytes
    • Infiltrate predominantly composed of CD3+ CD4+ alpha beta T cells
  • Mild to marked increase in intra-epithelial lymphocytes
    • Variable reports in the literature
    • Infiltrate predominantly composed of CD3+ CD4+ alpha beta T cells
  • Inconspicuous to prominent apoptosis in crypts
  • Crypts may be hyperplastic or destroyed
    • Goblet cells may be absent
  • Anti-enterocyte brush border antibodies demonstrable by indirect immunofluorescence
    • Anti-goblet cell antibodies may be present but less specific
  • May occur in at least three forms (Ruemmele 2008)
    • Associated with autoimmune endocrinopathy and mutations in FOXP3 gene leading to X-linkage, see IPEX syndrome
    • Same associations as IPEX syndrome except no X-linkage
    • Isolated autoimmune enteritis
  • Robert V Rouse MD
    Department of Pathology
    Stanford University School of Medicine
    Stanford CA 94305-5342

    Original posting/updates : 11/11/09, 11/20/11

Differential Diagnosis


Tropical Sprue

    • Confined to tropics
    • Responds to anti-microbial therapy


Prolonged Post-enteritis Syndrome

    • History of preceding viral or bacterial gastroenteritis


Celiac Disease Autoimmune Enteropathy
Usually occurs in childhood or older Usually begins under 6 months of age, but can occur in adults
Responds to gluten withdrawal Refractory to gluten withdrawal
Anti-endomysial and - tissue transglutaminase antibodies Anti-enterocyte antibodies
CD4 negative T cells predominate CD4+ T cells predominate
Gamma delta T cell receptors predominate Alpha beta T cell receptors predominate
For pediatric autoimmune enteropathy with associated polyendocrinopathy see IPEX syndrome.
Some adult autoimmune enteropathy cases have been discovered in the workup of patients thought to have celiac disease but who do not respond to removal of gluten from the diet


Autoimmune Enteropathy Common Variable Immunodeficiency – GI Involvement
Numerous plasma cells Plasma cells frequently markedly decreased
Diffuse infiltrate primarily composed of T lymphocytes Prominent nodular lymphoid hyperplasia
Prominent villous atrophy Villous atrophy may be mild to severe
Prominent crypt destruction Crypt destruction not prominent
Anti-enterocyte antibody All antibodies generally depressed; humoral testing is not reliable in CVID
The two entities may be histologically indistinguishable.
For pediatric autoimmune enteropathy with associated polyendocrinopathy see IPEX syndrome.


Food Protein Enteropathy Autoimmune Enteropathy
Predominantly eosinophilic infiltrate Predominantly T cell infiltrate
Frequent associated allergy or atopy No association with other allergies or atopy
Resolved by elimination of offending food from diet Not related to diet
For pediatric autoimmune enteropathy with associated polyendocrinopathy see IPEX syndrome.


Crohn Disease Autoimmune Enteropathy
Skip lesions predominate Usually diffuse
Usually involves large intestine Principal involvement is duodenum, jejunum and stomach
Transmural inflammation Mucosal inflammation
Granulomas may be seen Granulomas absent
Deep fissures frequent No fissures or deep ulcers
For pediatric autoimmune enteropathy with associated polyendocrinopathy see IPEX syndrome.


  • Usually presents <6 months of age
    • Intractable diarrhea
    • Non-responsive to TPN
    • 30% mortality
  • Rarely presents in adults, usually with some other autoimmune disorder
    • Many adult cases present as celiac disease that is not responsive to gluten free diet
    • May be associated with thymoma
  • Extra-intestinal associations
    • Insulin dependent diabetes mellitus
    • Hypothyroidism
    • Membranous glomerulonephritis
    • Sclerosing cholangitis
    • Autoimmune hepatitis
    • Coombs+ hemolytic anemia
    • Other autoantibodies
      • Anti-mitochondrial antibody
      • Anti-nuclear antibody
      • Anti-parietal cell antibody


  • Noffsinger A, Fenoglio-Preiser CM, Maru D, Gilinisky N.  Gastrointestinal Diseases, AFIP Atlas of Nontumor Pathology, First Series, Fascicle 5, 2007.
  • Freeman HJ. Adult autoimmune enteropathy. World J Gastroenterol. 2008 Feb 28;14(8):1156-8.
  • Cuenod B, Brousse N, Goulet O, De Potter S, Mougenot JF, Ricour C, Guy-Grand D, Cerf-Bensussan N. Classification of intractable diarrhea in infancy using clinical and immunohistological criteria. Gastroenterology. 1990 Oct;99(4):1037-43.
  • Russo PA, Brochu P, Seidman EG, Roy CC. Autoimmune enteropathy. Pediatr Dev Pathol. 1999 Jan-Feb;2(1):65-71.
  • Akram S, Murray JA, Pardi DS, Alexander GL, Schaffner JA, Russo PA, Abraham SC. Adult autoimmune enteropathy: Mayo Clinic Rochester experience. Clin Gastroenterol Hepatol. 2007 Nov;5(11):1282-90.]
  • Carroccio A, Volta U, Di Prima L, Petrolini N, Florena AM, Averna MR, Montalto G, Notarbartolo A. Autoimmune enteropathy and colitis in an adult patient. Dig Dis Sci. 2003 Aug;48(8):1600-6.
  • Corazza GR, Biagi F, Volta U, Andreani ML, De Franceschi L, Gasbarrini G. Autoimmune enteropathy and villous atrophy in adults. Lancet. 1997 Jul 12;350(9071):106-9.
  • León F, Olivencia P, Rodríguez-Pena R, Sánchez L, Redondo C, Alvarez I, Moreira V, Roy G. Clinical and immunological features of adult-onset generalized autoimmune gut disorder. Am J Gastroenterol. 2004 Aug;99(8):1563-71.
  • Mais DD, Mulhall BP, Adolphson KR, Yamamoto K. Thymoma-associated autoimmune enteropathy. A report of two cases. Am J Clin Pathol. 1999 Dec;112(6):810-5.
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