Neurodegenerative diseases are disorders of the central nervous system caused by the progressive loss of structure and function of neurons – neurodegeneration. It is generally accepted that many neurodegenerative disorders are the result of genetic mutations, inflammation, misfolded proteins and environmental factors. Recently, the etiology of neurodegenerative diseases has been associated with microbial infections. Many studies have shown that gut microbiota can affect neurotransmitter levels, neurogenesis and the development of the central nervous system by regulating the concentration of brain derived neurotrophic factor. Microorganisms can also influence amyloidosis; abnormal aggregation of extracellular and intracellular proteins which contributes to the development of some neurodegenerative diseases, like Alzheimer’s and Parkinson’s disease. Gut microbiota has also been linked to autism, a neurobiological developmental disease, and multiple sclerosis. Although epidemiological observations and experiments on animal models support the hypothesis of the gut microbiota influence on the pathogenesis of neurodegenerative diseases through the gut-brain axis, there is still lack of clinical evidence. The influence of microorganisms on neurodegeneration is an interesting area for future research and it could help enlighten the origin and mechanisms of development of neurodegenerative disease and contribute to the finding of novel treatments.