The present study was performed to compare the effects on antioxidant activity and on DNA damage of organic and conventionally produced apples grown under controlled conditions in human peripheral blood lymphocytes. Six healthy volunteers consumed either organically or conventionally grown apples (Golden Delicious, 1000 g) from two neighboring commercial farms in a double-blinded, randomized, cross-over study. The average content of total identified and quantified polyphenols in the organically and conventionally produced apples was 308 and 321 microg/g fresh weight, respectively. No statistically significant differences in the sum of phenolic compounds or in either of the polyphenol classes were found between the agricultural methods. Consumption of neither organically nor conventionally grown apples caused any changes in antioxidant capacity of low-density lipoproteins (lag time test), endogenous DNA strand breaks, Fpg protein-sensitive sites, or capacity to protect DNA against damage caused by hydrogen peroxide. However, a statistically significant decrease in the levels of endonuclease III sensitive sites and an increased capacity to protect DNA against damage induced by iron chloride were determined 24 h after consumption in both groups of either organic or conventionally grown apples, indicating the similar antigenotoxic potential of both organically and conventionally grown apples.