BackgroundGenetic polymorphisms of antioxidant enzymes CAT, GPX, and SOD are involved in the etiology of obesity and its principal comorbidities. The aim of the present study was to analyze the effect of aforementioned SNPs over the output of several variables in people with obesity after a nutritional intervention. The study included 92 Mexican women, which received a dietary intervention by 3 months. Participants were genotyped and stratified into two groups: (1) carriers; mutated homozygous plus heterozygous (CR) and (2) homozygous wild type (WT). A comparison between CR and WT was done in clinical (CV), biochemical (BV), and anthropometric variables (AV), at the beginning and at the end of the intervention.ResultsParticipants (n = 92) showed statistically significant differences (p < 0.05) at the end of the nutritional intervention in several CV, BV, and AV. However, two kinds of responses were observed after genotyping participants: (A) CR and WT showed statistically significant differences (p < 0.05) in several CV, BV, and AV for the SNPs 599C>T GPX1 (rs1050450), − 251A>G SOD1 (rs2070424), and − 262C>T CAT (rs1001179). (B) Only CR showed statistically changes (p < 0.05) in several CV, BV, and AV for the SNPs − 21A>T CAT (rs7943316) and 47C>T SOD2 (rs4880). The dietary intervention effect was statistically significantly between the polymorphisms of 47C>T SOD2 and BMI, SBP, TBARS, total cholesterol, and C-LCL (p < 0.05) and between the polymorphisms of − 21A>T CAT (rs7943316) and SBP, DBP, total cholesterol, and atherogenic index (p < 0.05).ConclusionPeople with obesity display different response in several CV, BV, and AV after a nutritional intervention, depending on the antioxidant genetic background of SOD and CAT enzymes.