In this article, we focus on children who have been diagnosed with autism spectrum disorder (ASD) and also have gastrointestinal (GI) issues. In particular, we are interested in the connection between GI issues, the microbiome, and ASD-related symptoms. We put forward the concept that diets recently shown to be advantageous in managing chronic digestive ailments such as Crohn’s disease and irritable bowel syndrome (IBS) have components that may benefit a subset of children with autism. In addition, we see a (not too distant) day in which behavioral problems often associated with ASD, particularly irritation, aggression, and self-harm, are well managed by a variety of interventions that modulate the microbiome.