Abstract Objectives DNA repair mechanisms work insufficiently in T2DM patients and hyperglycemia seen in diabetes disturbs the oxidant-antioxidant balance thus cause oxidative damage on DNA. The effects of the DNA repair genes’ have not yet been investigated on diabetes. The aim of this study was to investigate the association between APE1 Asp148Glu and XPG Asp1104His polymorphisms with T2DM in the Turkish population. Material and methods Sixty-five T2DM patients and 54 healthy individuals were included to this study as control. The polymerase chain reaction-restriction fragment length polymorphism techniques were used. Results When the study groups were compared, serum HDL-cholesterol levels were found statistically elevated in the controls. Once the APE1 Asp148Glu polymorphism distribution between the patient and control groups was investigated, the Glu/Glu genotype ratio was found significantly higher in the control group. Furthermore, the Asp/Glu genotype and the Asp allele prevalences were observed to be higher in the patient group. Also, patients with the Asp/Asp genotype had higher serum HDL-cholesterol levels than the others. Conclusion Despite the small number of subjects included, it could be interpreted that the Glu allele of the APE1 Asp148Glu polymorphism might be protective against and the Asp allele may be contributing to the development of diabetes.