CNS disorders represent a heterogeneous group of disorders that include both neurological and psychiatric entities. With the global increase in prevalence of depression particularly, but also Alzheimer's dementia and disorders of pervasive developmental disturbance spectrum, CNS disorders are increasingly coming to focus of the medical and wider community. Through the access to new technologies such as next generation sequencing, proteomics, metabolomics and other tools of P4 medicine, new possibilities arise for prevention, early detection, diagnosis and treatment of all diseases, including CNS disorders. Among the mechanisms of maintenance of the homeostasis of the human organism, the maintenance of microbiota homeostasis is of importance, too, and novel scientific questions about the role of human microbiota in both health and illness of its host arise. Numerous roles of human intestinal microbiota have already been discovered, from intestinal barrier maintenance, neurotransmitter production, role in the immune system, modulation of the HPA axis etc. to its role in CNS disorders. The human digestive system is in many ways associated with the CNS, through the so-called gut-brain axis whose whole potential has only recently been discovered by learning about the crucial role of microbiota in its mechanisms. Many researches bring interesting insight into the many common characteristics of nutritional profiles of patients suffering of the same CNS disorders, such as frequent gluten and casein hypersensitivity in schizophrenia and childhood autism, disturbance in microbiota homeostasis in depression, childhood autism and Parkinson disease, ω-3 fatty acids deficiency, vitamin D deficiency, folate deficiency in schizophrenia and depression, the benefit of natural polyphenols in Alzheimer's disease, the role of the gut-brain axis in Parkinson disease, etc. New possibilities arise when it comes to treating these disorders via nutritional interventions and future translation into clinical practice will most certainly provide more comprehensive and higher standards of quality care for the patients.