Flavonoids: quercitrin, myricitrin and rutin and their metal complexes were comparatively investigated for binding to DNA by means of spectrophotometric methods and DNAse activities were evaluated via agarose gel electrophoresis of pBR322. Free flavonoids bind to DNA in an intercalative mode, but Cu(II) complexes of these flavonoids bind even stronger due to the electrostatic interaction of the metal in addition to the intercalation. Flavonoids show protective effect against DNA cleavage in the presence of peroxide. However, Cu(II) and Zn(II) complexes of these flavonoids cause multiple scissions on the DNA backbone. In addition, Cu(II) complexes of the flavonoids have stronger DNAse activity. Moreover, myricitrin was found two times more cytotoxic when combined with metal ions (Cu-2+ or Zn2+) than when used alone against peripheral blood mononuclear cells.