We have investigated separate as well as combined influence of IL-1beta TaqI, IL-1ra VNTR and CTLA-4 + 49 A/G polymorphisms on susceptibility, clinical course and progression of MS in 162 Serbian patients. We found significant independent relative risk for MS susceptibility in noncarriers of IL-1ra allele 2 (OR = 2.2, CI = 1.3-3.7, p = 0.003) and CTLA-4 + 49 AA genotype (OR = 2.0, CI = 1.2-3.5, p = 0.01) as well as their combined effect (OR = 4.4, CI = 2.0-9.7, p = 0.0003). Our result supports the significant and combined effect of IL-1ra VNTR and CTLA-4 polymorphisms on MS justifying the need for further haplotype analysis in different populations.