The underlying biology of Autism Spectrum Disorders (ASD) may contribute significantly towards disease comorbidity. Gastrointestinal symptoms represent an important comorbidity in children with ASD and may also contribute directly towards their problem behaviors. Gastrointestinal symptoms often pose a dilemma to care providers because the presentation and cause in this population is ill defined and especially difficult to detect in children with limited verbal communication. This multi-site collaborative project is focused on identifying stool based biomarkers of gastrointestinal symptoms in children with ASD. This effort is based upon innovative findings that certain disease biomarkers are evident across a spectrum of gastrointestinal symptoms while absent in healthy individuals. Behavioral characterization of participants with ASD will allow evaluation of associations between specific behavioral traits, gastrointestinal disease profiles, and multi-omic (microbiome and metabolome) stool signatures. The ultimate goal of this project is to correlate stool biomarkers with behavioral traits in individuals with ASD and functional gastrointestinal disorders to help improve in the diagnosis of symptoms in children with ASD. Identification of correlates between clinical metadata and functional alterations in the microbiome may rapidly justify microbial manipulation as early therapy in children newly diagnosed with ASD.