Gastrointestinal (GI) dysfunction is a common comorbidity of autism spectrum disorders (ASD) and is associated with increased severity of characteristic autism-associated symptoms. However, the underlying biological mechanisms for GI dysfunction symptoms in children with ASD are unknown. This review explores potential explanations for these symptoms including altered enteric microbiota, impaired intestinal permeability, changes in immune homeostasis, and genetic factors such as single nucleotide polymorphisms. It was shown that genetic factors not only influence the development of altered enteric microbiota and impaired intestinal permeability, but also are a strong, independent contributor to GI dysfunction in ASD patients.