Background: Multiple sclerosis (MS), as a multifactorial autoimmune disease with complex genetic basis, causes demyelination in the central nervous system via cytokine responses to myelin antigens. Myelin basic protein (MBP) is the main protein component of the myelin sheath. HLA-DRB (human leukocyte antigen-DR beta) alleles, particularly HLA-DRB1*1501, may be of significance in the pathogenesis of MS. Objective: To examine the association of HLA-DRB1*1501 alleles and MBP VNTR (variable number tandem repeat) polymorphism with the MS susceptibility in Iranian population. Methods: Genomic DNA was extracted from peripheral blood. The alleles were determined by the Polymerase Chain Reaction (PCR) method in 259 MS patients and 312 healthy control individuals and analyses were carried out using Fisher's exact test. Results: The frequencies of MBP VNTR genotypes (AA, AB and BB) were 47%, 42% and 11% among patients, and 45%, 43% and 12% in control subjects, respectively. HLA-DRB1*1501 allele was more frequent among patients than healthy individuals (OR=1.65, P=0.0045). The frequency of allele A and genotype A/A was significantly higher among HLA-DRB1*1501 positive patients (61% and 32%) than controls (46% and 19%) (OR=1.88, P=0.0013; A/A vs. B/B: OR=5.09, P=0.0004). The two-locus analysis of the interaction between the MBP VNTR polymorphism and the HLA-DRB1 allele showed that the HLADRB1* 1501/A haplotype was more frequent among MS patients than the healthy controls. Conclusion: The interaction between the HLA-DRB1*1501 allele and MBP gene may be considered as a predisposing factor in the development and pathogenesis of MS in the case of gene-gene interaction.