We report here a study using a model of multiple sclerosis – experimental allergic encephalomyelitis (EAE) – to investigate changes in the qualitative and quantitative composition of the intestinal microbiota in rats with disease symptoms and with a symptom-free course. When clinical symptoms of EAE were apparent, there were changes in the composition of the microbiota of the gastrointestinal tract, with increases in the numbers of Gram-negative opportunistically pathogenic bacteria: Citrobacter spp., Klebsiella spp., and atypical E. coli. Rats without clinical signs of EAE were also found to have increased contents of Faecalibacterium prausnitzii. The significance of complexes changes in the composition of the intestinal microbiota is discussed, as this provides evidence of prolonged persistence of dysbacteriosis in rats on developing EAE.