Systemic oxidative stress plays a role in many degenerative diseases. Although regular physical activity has been known as the most effective non-pharmacological intervention to alleviate the oxidative stress, the beneficial effect varies between individuals.We investigated whether NADPH oxidase p22phox gene C242T and A640G polymorphisms are associated with systemic oxidative stress level response to exercise training (EXTR). Fifty-nine sedentary middle-age to older Caucasians with relatively high cardiovascular disease (CVD) risk factors underwent a six-month standardized exercise training program. Body mass index, plasma lipoprotein-lipid profiles, cardiovascular fitness (VO₂max), and plasma thiobarbituric acid reactive substances (TABRS) were measured before and after EXTR. Demographic and initial levels of CVD risk factors were similar among genotype groups for both polymorphisms. Overall, TBARS was decreased by 16% with EXTR in the entire group (P < 0.001). There was no significant difference in TBARS changes with EXTR among the C242T genotype groups. However, A allele carriers showed greater reduction in TBARS than non-carriers at the A640G locus (P = 0.05). There was a significant interaction (P = 0.05) between EXTR and A640G polymorphism in TBARS changes with EXTR. This interaction remained after accounting for age and baseline TBARS level. Furthermore, diplotype analysis showed that TBARS was decreased to a greater extent in the C242/A640 haplotype carriers compared to the non-carriers (P < 0.05). We found that p22phox polymorphisms, especially A640G, were associated with differential changes in systemic oxidative stress with aerobic exercise training.