<b><i>Background:</i></b> We aimed to detect single nucleotide polymorphisms (SNPs) and mutations in DNA repair genes and their possible association with myelodysplastic syndrome (MDS). <b><i>Methods:</i></b> Targeted enrichment resequencing of 84 DNA repair genes was initially performed on a screening cohort of MDS patients. Real-time polymerase chain reaction was used for genotyping selected SNPs in the validation cohort of patients. <b><i>Results:</i></b> A heterozygous frameshift mutation in the <i>XRCC2</i> gene was identified. It leads to the formation of a truncated non-functional protein and decreased <i>XRCC2</i> expression level. Decreased expression levels of all DNA repair genes functionally connected with mutated <i>XRCC2</i> were also present. Moreover, a synonymous substitution in the <i>PRKDC</i> gene<i></i> and 2 missense mutations in the <i>SMUG1</i> and <i>XRCC1</i> genes were also found. In the screening cohort, 6 candidate SNPs were associated with the tendency to develop MDS: rs4135113 (TDG, p = 0.03), rs12917 (MGMT, p = 0.003), rs2230641 (CCNH, p = 0.01), rs2228529 and rs2228526 (ERCC6, p = 0.04 and p = 0.03), and rs1799977 (MLH1, p = 0.04). In the validation cohort, only a polymorphism in <i>MLH1</i> was significantly associated with development of MDS in patients with poor cytogenetics (p = 0.0004). <b><i>Conclusion:</i></b> Our study demonstrates that genetic variants are present in DNA repair genes of MDS patients and may be associated with susceptibility to MDS.