Multiple sclerosis (MS) is an inflammatory disease of the central nervous system, with disturbances of the immunological balance. As TLR9-null mice showed increased resistance to experimental autoimmune encephalomyelitis and recent genetic investigations showed that T-1237C promoter polymorphism of TLR9, commonly implicated in autoimmune diseases, induces a deregulation of its expression, we performed an association study in a Portuguese population of 165 MS patients and unrelated healthy controls. Our results show no significant association with MS and no protective effect of T-1237C concerning age of onset, disease severity or disease subtype in MS patients.