Autism Spectrum Disorder (ASD) is a neurodevelopment disorder characterized by impairment in social interaction, communication, and behavior, as well as sensory challenges. In addition, secondary symptoms can appear, such as gastrointestinal disorders. Gut microbiota has an important role in the harvest of nutrients and energy from our diet. It influences a wide range of metabolic, developmental, and physiological processes such as the maintenance of the gut epithelial layer, immune system development, protection against pathogens, detoxification and xenobiotics degradation. The ecosystem of a healthy human gastrointestinal (GI) tract is mainly populated by Firmicutes and Bacteroidetes phyla, to a lesser extent by Actinobacteria and Proteobacteria, in this case the microbiota is in an eubiosis condition. Whether a disturbance of the microbial ecosystem occurs, gut microbiota is in a dysbiosis condition and it could lead different metabolic disorders. The two-way communication between gut microbiota and central nervous system (CNS) affects stress response, pain perception, neurochemistry and several disorders. The gut microbiota in ASD patients revealed some peculiarities such as the high percentage of Propionibacter and Clostridium, well known for their production of pro inflammatory metabolites, or an increment of Sutterella spp. and Ruminococcus torques, which are negatively associated with the health of the gut. Recent studies suggest that also the oral microbiota may be involved in ASD symptoms assuming the existence of a microbiota-oral-brain axis. ASD patients are often suffering of several oral cavity disorders like caries, gingivitis and periodontitis, probably due to the poor oral hygiene. These disorders are linked to a dysbiosis of the oral microbiota: the characterization of the ASD subjects oral microbiota showed a lower biodiversity of bacteria species and different levels of specific bacteria, comparing to the controls. Several studies suggest that some bacteria species invade the blood-brain barriers as well as their metabolites, triggering inflammatory response and an alteration of the metabolic activity in the CNS. It has been demonstrated that ASD patients have a high level of pro-inflammatory cytokines and chemokines in the cerebrospinal fluid and an upregulation of the microglia. The oral microbiota could also affect the lower GI tract and have a significant role within the ASD-associated GI disorders and CNS inflammation