In an opinion piece in The New York Times, 8/25/12, called "An Immune Disorder at the Root of Autism", the author Moises Beasquez-Manoff discusses research that shows that perhaps one-third of cases of autism are caused by immune dysregulation related to the mother's response to inflammation during pregnancy. Results of a study in Denmark, for instance, indicate that viral infections in the mother during pregnancy increases the chances of having an autistic child by 30% and bacterial infections by 40%.
Infection is unlikely to have caused the increased incidence in cases of autism directly, because we are "more infection free than any other time in history". Instead, the increase parallels other epidemics like asthma and other autoimmune diseases. Autism seems linked to the autoimmune diseases of the mother:
"…One large Danish study, which included nearly 700,000 births over a decade, found that a mother’s rheumatoid arthritis, a degenerative disease of the joints, elevated a child’s risk of autism by 80 percent. Her celiac disease, an inflammatory disease prompted by proteins in wheat and other grains, increased it 350 percent. Genetic studies tell a similar tale. Gene variants associated with autoimmune disease — genes of the immune system — also increase the risk of autism, especially when they occur in the mother."
Theories to explain the increase in autoimmune diseases include the hygiene hypothesis — that we suffer from "microbial deprivation" and that in cultures with more exposure to microbes and parasites there are fewer autoimmune diseases. Animal studies also support some of the theories proposed in this article.
These studies provide a "therapeutic target" for treatment of autism and further research.