We know that the bacterial colonization plays a key role for the intestinal health, but we now know that the intestinal bacterial flora may also be involved in other areas. Over the past ten years the research has increasingly focused on the role of the microbiota of the gut and colon in the modulation of the brain function, mainly in animal models. New clinical and preclinical evidence identify the microbiome as a possible key susceptibility factor for neurological disorders, including Alzheimer’s disease, autism spectrum disorder, multiple sclerosis, Parkinson’s disease, and stroke. Even if cross-sectional clinical studies support the contribution of altered microbial composition to the pathophysiology of such diseases, interpretation of data is often difficult because the composition of the microbiome is influenced by various factors such as diet and exercise.