Background: The gastrointestinal tract and the central nervous system are distinct because of evident morpho-functional features. Nonetheless, evidence indicates that these systems are bidirectionally connected through the gut-brain axis, defined as the signaling that takes place between the gastrointestinal tract and central nervous system, which plays in concert with the gut microbiota, i.e., the myriad of microorganisms residing in the lumen of the human intestine. In particular, it has been described that gut microbiota abnormalities, referred to as dysbiosis, may affect both central nervous system development and physiology. Objective: Starting from the possible mechanisms through which gut microbiota variations were found to impact several central nervous system disorders, including Autism Spectrum Disorder and Alzheimer’s Disease, we will focus on intriguing, although poorly investigated, aspects such as the epithelial and vascular barrier integrity. Indeed, several studies suggest a pivotal role of gut microbiota in maintaining the efficiency of both the intestinal barrier and blood-brain barrier. In particular, we report evidence indicating an impact of gut microbiota on intestinal barrier and blood-brain barrier homeostasis and discuss the differences and the similarities between the two barriers. Moreover, to stimulate further research, we review various tests and biochemical markers that can be used to assess intestinal and blood-brain barrier permeability. Conclusion: We suggest that the evaluation of intestinal and blood-brain barrier permeability in neurological patients may not only help to better understand central nervous system disorders but also pave the way for finding new molecular targets to treat patients with neurological impairment.