Disclosed is a method of diagnosing autoimmune diseases, such as multiple sclerosis and systemic lupus erythematosus, which involves detecting the presence of small intestinal bacterial overgrowth (SIBO) in a human subject having at least one symptom associated with a suspected diagnosis an autoimmune disease. Also disclosed is a method of treating these autoimmune diseases, which involves at least partially eradicating a SIBO condition in the human subject. The method includes administration of antimicrobial or probiotic agents, or normalizing intestinal motility by employing a prokinetic agent. Also disclosed is a kit for the diagnosis or treatment of autoimmune diseases.
