Introduction: Previous studies revealed that oxidative stress is elevated in multiple sclerosis (MS). It can harm to biological macromolecules such as DNA. However, the molecular mechanism in protection of genetic information from DNA damages is not clear in MS disease. In this study the expression level of some important genes of OGG1 and MYH involved in base excision repair pathway and, MTH1 and ITPA as main cleaning genes of nucleotide pool from rough nucleotides are examined in MS patients in compared to healthy group. Methods: Peripheral blood mononuclear cells were isolated from relapsing-remitting-MS patients and healthy subjects. After RNA extraction and cDNA synthesis, the expression levels of target genes were examined by RT-qPCR technique. Results: The level of the MTH1 and MYH genes expression were decreased, but the level of OGG1 mRNA was higher in patients in comparison to the control group. Obtained result did not shown any correlation between expression of examined genes and clinical features of patients such as MS severity and disease duration. Conclusion: These preliminary results provide more supportive evidences for involvement of oxidative damage and variation in expression of DNA repair genes in MS. Significant increase of OGG1 suggest that the development and progression of pathogenesis in Iranian MS can be related to chronic and direct oxidative damage of genomic DNA not nucleotide pools.