Many if not all autistic children have a damaged intestine/gut. The damage may be there from birth but more likely comes from some immunological injury like a bad reaction to an immunization. (Keep in mind this is mostly theory). Autistic children seem to have weaker immune systems, and a lot seem to have digestive problems.
This "leaky gut" allows some food proteins to pass through into the bloodstream only partially digested, particularly the gluten from wheat/oats/rye/barley, and the casein from milk and other dairy products. These partially digested proteins form peptides which have an opiate-like affect (opioids is another term for them). They can bind to the receptors and cause harmful effects in the brain just like a regular opiate. Opiates can either cause or magnify autistic symptoms. The opiates are a type of narcotic. There are receptors in the brain that they bind with to reduce pain and induce pleasure, but they also have harmful side effects. An example of an opiate is morphine or heroin. Until it can be figured out how to heal the "leaky guts", many parents are putting their children on the gluten free/casein free diets.
A gluten-free casein-free diet (or GFCF diet) eliminates intake of the naturally-occurring proteins gluten (found naturally in wheat, barley, spelt, triticale, kamut, rye and possibly oats) and casein (found in milk). The Autism Research Institute and other advocacy groups recommend the diet as a treatment for autism and related disorders. Studies supporting these claims have had significant flaws, and the data are inadequate to guide treatment recommendations. Moreover, studies have found that such diets can lead to nutrient deficiencies that weaken bone structure, increasing the risk of broken bones.
Removing gluten and casein from a child's diet is not as simple as saying goodbye to milk and bread. According to Carol Ann Brannon, a nutritionist who specializes in diets for children with autism, gluten is not only ubiquitous, but may also find its way into your child's system through the skin.
In general, says Brannon, "Children can eat a wide variety of meat, chicken, eggs, fruits, and vegetables -– anything that does not contain wheat gluten or casein. It is generally recommended that organic, whole GFCF foods be consumed whenever possible."