Evidences from animal models and humans have implied the involvement of alterations in the gut microbiota in development of some autoimmune diseases. Dysbiosis observed in autoimmune diseases is associated with decreased bacteria function and diversity, impaired epithelial barrier function, inflammation, and decreased regulatory T cells in the gut mucosa. Studies suggest that probiotics influence systemic immune responses, ensure the homeostasis of the healthy microbiota in the intestinal mucosa, and could, therefore, be used as adjuvant therapy to treat immune-mediated diseases. The mechanisms proposed to achieve this include mucus secretion; antimicrobial peptide production; the maintenance of the function of the gastrointestinal-epithelial barrier, ensuring adequate interactions between the gut microbiota and the mucosal immune cells; and, finally, helping the activation of host immune system in response to pathobionts. Here, we described several reports concerning probiotic applications in several animal models of autoimmune diseases and data of the main clinical trials concerning the applicability of probiotics in type 1 diabetes, multiple sclerosis, rheumatoid arthritis, and systemic lupus erythematosus.