The aim of this study was to assess the possible influence of genetic polymorphisms in hOGG1, XRCC1, XRCC3, XPD, XPG and APE1 on the observed DNA damage in a group of Turkish myelodysplastic syndrome (MDS) patients. A total of 39 patients with myelodysplastic syndrome and 78 age-matched healthy control subjects were included in our study. Polymerase chain reaction/restriction fragment length polymorphism analysis was performed for the detection of DNA repair gene variants. No significant differences in DNA repair enzymes APE1, XRCC1 and XPG were found between MDS patients and controls. On the other hand, XRCC3, XPD and hOGG1 were associated with an increased risk of MDS (p = 0.004, p = 0.000, p = 0.017, respectively). Specifically, Thr/Met genotype was more relevant in patients (p = 0.026) in XRCC3; in hOGG1, Cys+ genotype was found higher in patients (p = 0.017); and in XPD, Gln/Gln genotypes were found higher in the patient (p = 0.001). In conclusion, XRCC3, XPD and hOGG1 genotypes are associated with an increased MDS risk, suggesting their possible involvement in the pathogenesis and biology of this disease.