Background: Polymorphisms in glutathione S-transferase (GST) genes may contribute to breast cancer risk. The aim of this study was to investigate any association of two common GSTO1 A140D and GSTO2 N142D gene polymorphisms with breast cancer risk in an Iranian population followed by a protein structure analysis. Materials and Methods: In the case-control study, 303 subjects comprising 153 women with breast cancer and 150 healthy controls were included. Genotypes of GSTO1 A140D and GSTO2 N142D polymorphisms were assessed by PCRRFLP. Bioinformatics tools were employed to evaluate the damaging effects of A140D and N142D on the structures of GSTO1 and GSTO2 proteins. Results: Our genetic association study revealed that the GSTO1 A140D polymorphism was associated with breast cancer in a dominant model (OR= 1.75, 95%CI= 1.07-2.86, p= 0.026). Also, the A allele was significantly associated with breast cancer risk (OR= 1.69, 95%CI= 1.09-2.60, p= 0.018). With regard to the N142D polymorphism, there were significant associations between the GG genotype (OR= 2.20, 95%CI= 1.14-4.27, p= 0.019) and the G allele (OR= 1.47, 95%CI= 1.06-2.05, p= 0.021) and risk of breast cancer. Structural analysis revealed that A140D and N142D polymorphisms cause changes in both primary and secondary structures of GSTO1 and GSTO2, respectively. Conclusion: Based on our results, GSTO1 A140D and GSTO2 N142D polymorphisms could be genetic risk factors for breast cancer, but further studies with larger sample sizes focusing on different ethnicities are needed to obtain more comprehensive results.