Background: The interactions of small molecules with nucleic acids are of considerable interest for the design of novel anticancer compounds. The physical properties and sequence specificity observed in the interactions between a group of flavonoids with proven antitumour activity and various nucleic acid structures are summarised. Materials and Methods: UV and fluorescence spectroscopy, together with competition dialysis, were used to assess the affinity of the drugs for the nucleic acid structures in the presence or absence of different metal ions. The effect of these compounds on breast and leukaemia cancer cell lines was evaluated using MTS and COMET assays and flow cytometry. Results and Conclusion: The flavonoids studied are weak duplex DNA-binding ligands and the binding of flavonoids to DNA is affected by metal ions. Baicalein and quercetin display stronger affinity for triplex and quadruplex than for double-stranded DNA and offer interesting scaffolds for the design of novel, high order DNA-binding agents.