Following upon the discoveries that specific bacteria in the gut may modulate the onset of experimental autoimmune encephalomyelitis, an animal model for MS, the human gut microbiota has been investigated in multiple sclerosis (MS). Data have been mostly generated from small to moderate size studies using stool samples from patients with relatively long disease duration and often receiving disease-modifying therapies that can affect microbial communities. The alpha and beta diversity of these microbial communities appears overall similar in patients and controls. In contrast, increased or decreased abundance of various taxa have been reported in cases, some of which are consistent across studies. Very few publications have addressed so far the association between the gut microbiome characteristics and the risk of relapse or disability progression. The change in gut microbiome function resulting from alterations in microbial communities (i.e. the dysregulation of specific metabolic pathways due to variation in the presence or abundance of specific taxa) is now more actively studied in inflammatory CNS disorders. Ongoing pilot trials of probiotic supplementation or microbiome transplant will determine the feasibility of these interventions.