Charlie is on a diet free of gluten, casein, corn and soy. In addition, we follow a Feingold diet, so no food colours, preservatives, flavours, msg etc.   For more info on these diets, check out the research.

Dr. Dohan was the first to discover a connection between celiac and schizophrenia. Or the first to suggest a gut-brian connection.
http://www.uthsc.edu/neuroscience/faculty/C_Dohan.php

Dr. Feingold discovered a connection between additives, colours, flavours and artificial sweetners and ADHD
http://www.feingold.org/

This is the most comprehensive guide to the gfcf diet.
http://www.gfcf.com/

A Canadian reseracher has discovered a connection between proprionic acid and autism, this acid is produced by enterobacteria and also added to many foods as a preservative to inhibit mold and bacteria growth.
http://psychology.uwo.ca/pdfs/autism/MacFabe%20etal07.pdf

This research group from Sunderland University are conducting double blind controlled studies on the gfcf diet.  They support the opiodpeptide theory.  This is similar to the leaky gut hypothesis, or that a damaged intestinal wall and unhealthy gut microflora are allowing partially digested proteins, or peptides into the blood stream.  The peptides from gluten and casien mimic morphine and have a drug-like effect on the brain.
http://www.espa-research.org.uk//

I cook everyday from scratch, but often rely on baking mixes and store bought baked goods.

I implemented the gfcf diet the day after we received an Aspergers diagnosis on Feb 13 2011. The behavior change was immediate. Less aggression, especially towards us before and after meal times. His social communication improved, he started to toilet train, and stopped craving baked goods. The most amazing thing happened when I took him grocery shopping for the first time after the diet change. Instead of demanding cupcakes he requested radishes and fish. Even now when I go grocery shopping he asks for fish. I've been using the Seachoice iPhone app to help me select fish that has the least toxins, and is environmentally sustainable. This week I bought some wild pickerel from the Dupont Christie Loblaws and pan fried it with rice flour and made a gfcf mushroom sauce served with zucchini, carrots and rice. He loved it and had seconds.