Multiple sclerosis (MS) is thought to be an autoimmune T-cell-mediated disease directed at myelin antigens of the central nervous system. Besides myelin proteins, lipid components of CNS are supposed to playa role as antigens for T cells in MS. CDI is a family of MHC-like glycoproteins specialized in capturing and presenting a variety of microbial and self lipids and glycolipids to antigen-specific T cells. CD L-restricted T cells specific for gangliosides and sulfatide have been isolated from subjects with MS and in mice with experimental allergic encephalopathy. We genotyped exon 2 of CDIA and CDIE in 205 MS patients and 223 unrelated healthy controls and determined their association with the presence of anti-ganglioside and anti-sulfatide antibodies. CDIE 01-01 is associated with a reduced risk ofMS (OR 0.54, p=O.OOI); CDIA 02-02 (OR 1.99, p=0.012) or CDIE 02-02 (OR 2.45, p=O.OOO) with an increased risk. The combination of the genotypes CDIA 02-02 and CDIE 02-02 is present in 90.7% of patients but in only 9.4% controls (OR 94.16, p= 0.000). CDIA and CDIE polymorphisms contribute to the polygenic susceptibility to MS. The functional effects of CDI polymorphisms are unknown, however changes in CDI alleles may affect numerous immunological functions.Multiple Sclerosis (MS) is a complex demyelinating disorder ofthe central nervous system (1). Environmental influences and genetic factors are implicated in the risk of developing MS. The idea that genetic factors may playa role in MS was first raised in the 1890's with the identification of familial aggregation (2). The data from twin studies indicate a strong familial factor in MS, with a concordance rate for monozygotic twins of about 20% (range 0-40%) (3). More than 20 whole genome studies have been performed employing up to 6,000 microsatellite markers and different methodologies in different MS populations (4). The strongest association was found for one or more susceptibility genes on chromosome 6p21 in the area of the major histocompatibility complex (MHC) (5). More recently, genome-wide association studies have described polymorphisms within genes related to the regulation of the immune response not MHC-dependent (6). All the newly identified MS risk alleles are common, exert only modest individual effects on risk (odds ratios 1.1-1.3) and act independently (6).