Abstract A recent meta-analysis of genome-wide association screens coupled to a replication exercise in a combined US/UK collection led to the identification of 4 single nucleotide polymorphisms (SNPs) in three gene loci, i.e. TNFRSF1A , CD6 and IRF8 , as novel risk factors for multiple sclerosis with genome-wide level of significance. In the present study, using a combined all-Spain collection of 2515 MS patients and 2942 healthy controls, we demonstrate significant association of rs17824933 in CD6 ( P CMH = 0.004; OR = 1.14; 95% CI 1.04–1.24) and of rs1860545 in TNFRSF1A ( P CMH = 0.001; OR = 1.15; 95% CI 1.06–1.25) with MS, while the low-frequency coding non-synonymous SNP rs4149584 in TNFRSF1A displayed a trend for association ( P CMH = 0.062; OR = 1.27; 95% CI 0.99–1.63). This data reinforce a generic role for CD6 and TNFRSF1A in susceptibility to MS, extending to populations of southern European ancestry.