Flavonoids are phenolic compounds, naturally found in vegetables, tea and red wines. A recent study has demonstrated that the flavonoids rutin and quercetin show a protective role against the deleterious effects of free radicals in cirrhotic rats. Considering this finding and the controversial results concerning the mutagenicity of rutin and quercetin recorded in the literature, the capacity of these flavonoids to cause damage to the DNA was evaluated using the alkaline single-cell gel electrophoresis (SCG) and micronucleus test in the bone marrow of mice. The doses for both compounds were 2 x 2500, 2 x 1250 and 2 x 625 mg/kg. Micronucleus test showed that rutin caused no damage to the DNA of the mice bone marrow cells, and the SCG assay demonstrated an increase of damage only at the dose of 2 x 1250 mg/kg. But when the mice cells of the three quercetin doses were compared with the negative control, significantly higher damage was observed by SCG assay, although not proportional to the dose. The micronucleus test also demonstrated a significant increase of damage, but only at the 2 x 1250 mg/kg dose. Considering the results obtained in this study with very high doses, it is unlikely that the consumption of rutin and quercetin produces any clastogenic effects. Our results also indicated that SCG could profitably be used in drug genotoxicity evaluation protocols.