When a child with celiac disease ingests foods that contain gluten proteins, their immune system responds by damaging their small intestine. Specifically, small finger-like projections that line the small intestine, called intestinal villi, are destroyed. Normally, food nutrients are absorbed through these villi to be carried into the bloodstream. When these villi disappear, the person absorbs the nutrients poorly and, malnutrition becomes a problem.

Most people digest gluten easily. However, a small part of the population is gluten intolerant, which is also known as celiac disease. Gliadin appears to be the protein that presents the biggest problem in celiac disease or gluten intolerance. Due to the fact that it is the body's own immune system that causes damage, celiac disease is considered to be an autoimmune disorder. However, it is also classified as a malabsorption disease, since the nutrients are not being absorbed.