Consumption of fruits and vegetables has been associated with a decrease in cancer incidence and cardiovascular disease, presumably caused by antioxidants. We designed a human intervention study to assess antioxidative and possible anti-genotoxic properties of fruit-borne antioxidants. We hypothesized that individuals bearing genetic polymorphisms for genes related to quercetin metabolism, B[a]P metabolism, oxidative stress, and DNA repair, differ in their response to DNA protective effects of increased antioxidant intake. In the present study, 168 healthy volunteers consumed a blueberry/apple juice that provided 97 mg quercetin and 16 mg ascorbic acid a day. After a four-week intervention period, plasma concentrations of quercetin and ascorbic acid, and total plasma antioxidant capacity (TEAC) were significantly increased. Further, we found 20% protection (p<0.01) against ex vivo H(2)O(2)-provoked oxidative DNA damage, measured by comet assay. However, the level of ex vivo induced BPDE-DNA adducts was 28% increased upon intervention (P<0.01). Statistical analysis of 34 biologically relevant genetic polymorphisms revealed that 6 significantly influenced the outcome of the intervention. Lymphocytes from individuals bearing variant genotype for Cyp1B1*5 seemed to benefit more than wildtypes from DNA-damage protecting effects upon intervention. Variants for COMT tended to benefit less, or even experienced detrimental effects from intervention. With respect to GSTT1 the effect is ambiguous: variants respond better in terms of intervention-related increase in TEAC, but wildtypes benefit more from its protecting effects against oxidative DNA damage. We conclude that genotyping for relevant polymorphisms enables selecting subgroups among the general population that benefit more of DNA damage-modulating effects of micronutrients.