The incidence of autism has been increasing at alarming rates in recent years. Effective therapies designed to address underlying factors contributing to this disorder will be discussed. An overview of the most common issues for children with autism will be presented including nutritional deficiencies, food sensitivities, mitochondrial dysfunction, gastrointestinal disorders, and environmental toxicity. Evidence-based treatment protocols, dietary modification, nutritional supplementation, and the role of comprehensive testing will be emphasized.