Interferon beta (IFN-β) and glatiramer acetate (GA) are the primary therapeutic immunomodulatory agents that interfere with relapsing-remitting multiple sclerosis (RRMS), and the most commonly-used drugs as well. Induction or aggravation of other immune-mediated diseases has been reported following INF-β administration. We have reviewed the reported cases to notify the treating physicians about these rare adverse events. Although co-morbid autoimmune disorders have been reported in patients with MS, the pro-inflammatory role of disease-modifying drugs, especially INF-β, could affect and enhance this co-occurrence. Clinical or laboratory autoimmunity histories suggest the use of GA over INF-β as the treatment of choice.