Currently intestinal microbiota is considered as a potential target for influence in various pathologies which have inflammation, autoimmunity or neurodegeneration in the genesis. Multiple sclerosis (MS) combines all these processes in the pathogenesis. Furthermore, the balance of the components of intestinal microbiota is disrupted during MS and followed by disbiosis. Different probiotics - bacteria with proven beneficial properties are widely used to correct dysbisis. In this paper, was investigated the ability of probiotic strain Enterococcus faecium L-3 to reduce disease severity in multiple sclerosis model - experimental allergic encephalomyelitis (EAE). E. faecium L-3 were used alone or in combination with glatiramer acetate (GA). It is shown that administration of E. faecium L-3 reduces the severity of EAE in rats almost as same as that of GA. However, when the probiotic enterococci administered together with GA the protective effect does not observed. It is assumed that these preparations stimulates different ways of the immune system, because their action stimulate different immune cells populations. The study demonstrates the ability of E. faecium L-3 to influence on the immune system in MS, directly and indirectly (through the correction of dysbiosis). This fact allows us to consider E. faecium L-3 as a potential tool for immunomodulation in autoimmune, inflammatory and neurodegenerative diseases.