Multiple sclerosis (MS) is a heterogeneous immune-related demyelinating disorder of central nervous system with several genetic and environmental factors contributing in its pathogenesis or patients' response to therapies. Myxovirus resistance protein A (MxA) is among the genes which are induced by IFNβ and are involved in the MS pathogenesis and/or response to IFNβ. In the present case-control study, we evaluated the association between three SNPs at nt -123 (A or C, rs17000900), nt -88 (G or T, rs2071430), and nt +20 (A or C, rs464138) and MS risk as well as treatment response in a population of Iranian MS patients including 146 IFNβ responders and 85 non-responders as well as 180 healthy controls. The AGA (-123, -88, +20) haplotype was more frequent in controls compared with MS cases (P = 0.038, OR (95% CI) = 1.77 (1.03-3.02)). Of particular note, the frequency of rs464138 AA genotype was significantly higher in responders compared with non-responders. However, the allele and genotype frequencies of other SNPs were not significantly different among patient subtypes or between patients and controls. Besides, we have demonstrated that CGC, ATA, and AGA (-123, -88, +20) haplotypes were significantly associated with IFNβ response in MS patients. As SNPs on MxA promoter region might participate in MS patients' response to IFNβ, prior patients genotyping may increase the rate of responsiveness and help in individualized selection of treatment options.