The intestinal microbiota is currently regarded as a potential target for treatments in many pathologies underlying the genesis of inflammation, autoimmune reactions, and neurodegeneration. Multiple sclerosis (MS) is a disease whose pathogenesis combines all these processes. MS also involves impairment to the balance between the components of the intestinal microbiota, with development of dysbiosis. Various probiotics are widely used to correct dysbiotic conditions – bacteria with proven useful properties. We report here the use of a model of multiple sclerosis – experimental allergic encephalomyelitis (EAE) – to study the ability of the probiotic Enterococcus faecium strain L-3 to decrease disease severity in rats when used alone and in combination with glatiramer acetate (GA). Administration of E. faecium L-3 was found to decrease the severity of EAE in rats to essentially the same extent as GA. However, simultaneous use of probiotic enterococci with GA produced no protective action. It is suggested that these agents stimulate different components of the immune system, as their actions produce increases in different populations of immune cells circulating in the blood. The study results demonstrate the ability of E. faecium L-3 to produce significant direct and indirect (via correction of dysbacteriosis) influences on the immune system in MS, which allows these bacteria to be regarded as a potential agent for immunocorrection in autoimmune, inflammatory, and neurodegenerative disease.