The purpose of this review is to summarize current knowledge about the gut microbiota in neuropsychiatric disorders. It is estimated that the human gut is colonized by up to 1018 microorganisms, mostly anaerobic bacteria. The gut microbiome is responsible for multiple functions, e.g. tightness of the intestine barrier, digestion and absorption. The correlation between gut dysbiosis and development of psychiatric, autoimmune and allergic diseases as well as bidirectional communication between brain and gut microflora have been shown. Recent findings suggest that specific bacteria can be involved in the development of clinical conditions, such as Autism Spectrum Disorders, depression and schizophrenia, and microbiota may be a target for therapeutic intervention providing novel treatment strategies.