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In a genetically predisposed individual of any age, the ingestion of even small quantities of foods containing gluten can trigger an immune response in the small intestine, causing chronic inflammation. This causes damage to the intestinal wall, resulting in a wide range of symptoms that vary from person to person.

In a healthy individual, the intestinal wall is covered with villi, the function of which is to increase the surface area of the intestine to aid in the absorption of nutrients. However, in celiac disease these villi are greatly reduced and the mucosal lining of the intestine is damaged. Because of the decrease in surface area, the absorption of nutrients such as protein, fats, carbohydrates, vitamins, and minerals is inhibited, leading to malnutrition and loss of function.