Autoimmune diseases are troubling, and often frustrating and painful for health care practitioners and patients. As far as I know, celiac disease is the only autoimmune disorder with a specific and identified trigger: the protein gluten. It has also been pointed out that the incidence of Celiac Disease, the formal name for gluten-triggered autoimmune reactions in the bowel, appears to have been increasing. Some have claimed that humans are not adapted to consumption of plant proteins like gluten, and that inflammatory bowel disorders are the result of the development of agriculture. However, there are a few other possibilities. One is that autoimmune disorders in general have been increasing and that Celiac disease is not increasing at a uniquely faster rate.
A major hypothesis in the development of allergies (inappropriate immune responses to non-pathogens, such as glutten or pollen or dog hair) is lack of exposure to potential allergens early in life. This, perhaps, is the root of the problem: soap, lysol, and a generally high level of cleanliness. Also, a huge change in human habit is the widespread introduction of infant formula to replace breast milk, and early introduction of other foods into infant diets. The ideal window of exposure to gluten is now considered to be between 4 and 7 months and that exposure should be concurrent with continuing breast milk consumption. Introduction to wheat cereals during this period is thought to be protective against celiac disease. Those raising their young children on gluten-free diets in the hope of protecting them from celiac disease, or the adverse effects of inflammation in general, may be taking the wrong route. (See Pinier et al. 2010 and Lopez-Serrano et al. 2010). Let them get a little dirty
Another possiblity, proposed by Elliot and Weinstock (2009) is the current rarity of helminth infection in the Western World. These authors propose that helminth infection was protective against autoimmune diseases like celiac disease by stimulating immune circuits that lower inflammation. I suppose if one were to choose between a gluten-free diet and helminth infection, most would go with the gluten-free diet. However, before you consider loss of bread as the price some pay for the protection of all against intestinal parasites, note that Elliot and Weinstock also propose exploration of the use of helminths for clinical treatment of auto-immune disease.
Elliott, DE and Weinstock JV (2009). Inflammatory bowel disease and the hygiene hypothesis: an argument for the role of helminths Progress in Inflammation Research, 149-178 DOI: 10.1007/978-3-7643-8903-1_9
Pinier M, Fuhrmann G, Verdu E, & Leroux JC (2010). Prevention measures and exploratory pharmacological treatments of celiac disease. The American journal of gastroenterology, 105 (12) PMID: 20877349
López-Serrano P, Pérez-Calle JL, Pérez-Fernández MT, Fernández-Font JM, Boixeda de Miguel D, & Fernández-Rodríguez CM (2010). Environmental risk factors in inflammatory bowel diseases. Investigating the hygiene hypothesis: a Spanish case-control study. Scandinavian journal of gastroenterology, 45 (12), 1464-71 PMID: 20704469