In genetically predisposed people gluten causes an autoimmune disease - they make antibodies which flatten the villi in the small intestine. This damage results in maladsorbtion of nutrients and leads to a condition called non tropical sprue and various other symptoms of a damaged intestine including gall stones and intestinal microbial imbalances. Also some people develop Dermatitis herpetaformis, a skin condition. I had all of the above and also Lyme Disease, swelling in my joints and symptoms of other auto immune problems. All of these problems have either disappeared or greatly improved on the gf diet. My body was so out of balance that it really helped to continue to do Clark's programs and other self treatments.
About 1% of people have this genetic problem with gluten although it is estimated that there are 3 to 4 million people in the US who are undiagnosed or misdiagnosed. The only treatment for Celiac Disease is strict avoidance of gluten.