The gut microbiota is a complex community of microorganisms located in a specific ecosystem, whose changes have a significant impact not only to various disturbances within that ecosystem, but also on diseases of central nervous system such as Alzheimer's disease and Parkinson's disease, amyotrophic lateral sclerosis and other neurodegenerative diseases. While the role of intestinal microbiota in the pathogenesis of gastrointestinal disorders such as ulcerative colitis and irritable bowel syndrome is already well understood, its role in the pathogenesis of neurodegenerative diseases has only been intensively investigated in recent years. The gut microbiota-brain axis is a two-way communication system that has not been fully explored, and includes various neurological, immunological, endocrinological and metabolic signaling pathways. Research on axenic animals indicates that the gut microbiota plays a significant role in the pathogenesis of neurodegenerative diseases. Dysbiosis-induced increased permeability of the gut and blood-brain barrier can affect the pathogenesis of various neurodegenerative diseases, especially those related to aging. Short-chain fatty acids play a significant role in the regulation of the brain and the behavior through G-protein-coupled receptors. Cytokines produced by cells of the immune system in the intestine affect the brain via the hypothalamic-pituitary-adrenal axis and the release of cortisol. Therapeutic options for the treatment of neurodegenerative diseases that would affect the gut microbiome are being investigated and there is evidence that some interventions have a benefical effect. The use of probiotics has led to improvement of symptoms in patients with neurodegenerative diseases, but there is also contradictory evidence, and recommendations for clinical use have not yet been developed.