Multiple sclerosis (MS) is an autoimmune disorder of multifactorial etiology. Family studies have shown strong genetic contributions. Linkage analyses have revealed several regions harboring risk genes including chromosome region 19q13. ILT6 is one of the most interesting candidate genes, since ILTs are involved in the generation of immunological tolerance. There is an absence/presence of variability of the ILT6 gene comprising several exons, thus incapacitating the gene function. In the present study, we examined the association of ILT6 deletion with MS. Using PCR typing, deficiency of ILT6 was examined in 607 blood donors and in 751 Caucasian German, as well as 89 French MS patients. Homozygous ILT6 deficiencies were significantly more prevalent in MS patients (7.1%) than in blood donors (3.8%; P=0.009). ILT6 deficiency is associated with MS in the German population and hence a likely risk factor for autoimmune disorders.