Basically, celiac disease is considered to be a genetic autoimmune disease caused by a permanent intestinal intolerance (allergy) to gluten that causes damage to the villi of the small intestine lining. The villi become inflamed, shortened and flattened resulting in the inability to absorb many nutrients. This can then effect the body in a large variety of ways (see Symptoms of Celiac Disease).

The classic pathology changes of celiac disease in the small intestine are categorized by the “Marsh classification”

• Marsh stage 0: normal mucosa
• Marsh stage 1: increased number of intra-epithelial lymphocytes, usually exceeding 20 per 100 enterocytes
• Marsh stage 2: proliferation of the crypts of Lieberkuhn
• Marsh stage 3: partial or complete villous atrophy
• Marsh stage 4: hypoplasia of the small bowel architecture

The changes classically improve or reverse after gluten is removed from the diet, so many official guidelines recommend a repeat biopsy several (4–6) months after commencement of gluten exclusion.
Stage 0 – A health intestine: