In this study, on the model of multiple sclerosis - experimental allergic encephalomyelitis (EAE), the dynamics of changes in the qualitative and quantitative composition of the intestinal microbiota in rats with symptoms of the disease and asymptomatic course were compared. It was found that the composition of the intestinal microbiota in rats with the clinical symptoms of EAE is shifted towards gram-negative opportunistic microorganisms of the genus Citrobacter, Prote- us, Klebsiella and enteropathogenic Escherichia coli. It has been shown that rats without clinical signs of EAE have higher levels of Faecalibacteriumprausnitzii. The significance of the complex changes in the composition of the intestinal microbiota, indicating long-lasting dysbiosis in rats during the development of EAE is discussing.