For some reason children with autism tend to have few beneficial bacteria compared to children without, and children with autism also have high levels of yeast as well. Yeast infection is not uncommon in children with autism.
According to Bright Tots, parents who have treated their children with antifungals report a drastic change in the childs behavior http://www.brighttots.com/Autism_Diet/Autism_Yeast_Diet. There are reasons for this belief, such as the beneficial bacteria will help with food allergens, or just because the body is not in balance, it has an effect on the brain toxins. Either way the positive benefits of Candida and Autism have not been proven, but what is experience by parents is what I would consider to be real.
To treat your child for Autism, I would use a natural approach. They are children, and if they have to take medication for years, you probably want to use the safest approach first. I think that once you put them on a diet where they can keep Candida under control, so they do not have to load up on medicines. While they are on the diet, ensure that your child with Autism get plenty of probiotics, as well as getting some natural Anti Fungals, goldenseal, Raw Garlic, Black Walnut, there are a multitude of antifungals that you can use.