The role of the intestinal microbiota and its influence on neurodegenerative disorders has recently been extensively explored, especially in the context of Parkinson's disease (PD). In particular, its role in immunomodulation, impact on inflammation, and participation in the gut-brain axis are under ongoing investigations. Recent studies have revealed new data that could be important for exploring the neurodegeneration mechanisms connected with the gut microbiota, potentially leading to the development of new methods of treatment. In this review, the potential roles of the gut microbiota in future disease-modifying therapies were discussed and the properties of the intestinal microbiota-including its impacts on metabolism and short-chain fatty acids and vitamins-were summarized, with a particular focus on atypical Parkinsonian syndromes. This review focused on a detailed description of the numerous mechanisms through which the microbiota influences neurodegenerative processes. This review explored potentially important connections between the gut microbiota and the evolution and progression of atypical Parkinsonian syndromes. Finally, a description of recently derived results regarding the microbiota alterations in atypical Parkinsonian syndromes in comparison with results previously described in PD was also included.