The aim of our work was to determine and to compare the possible antigenotoxic effect of methanolic extracts of common buckwheat (CB) and Tartary buckwheat (TB) flour, containing naturally present rutin (R), and quercetin (Q), and of R and Q in chemical form, against tert-butyl hydroperoxide (t-BOOH) induced DNA damage in human hepatoma cell line (HepG2). R and Q content of CB and TB flour extracts was determined by reversed phase-high performance liquid chromatography and antigenotoxic effect of flour extracts, R and Q was evaluated using the comet assay. R (100 μM) and Q (50 μM) decreased the extent of t-BOOH induced DNA damage for 51% and 67%, respectively. CB and TB flour extracts showed high antioxidant capacity and prominent genoprotective ability. CB extract containing up to 0.1 μM R decreased t-BOOH induced DNA damage for 34%, and TB extract containing up to 12.64 μM R, and 2.86 μM Q for 40%. The obtained results show high antigenotoxic activity of buckwheat and furthermore, they suggest that complex nutrient and flavonoid rich food products are more efficient in their health promoting effects compared to a single active substance.