DNA damaging agents are among the most powerful anticancer drugs currently in clinical use. As an alternative to irreversible nucleobase damage and DNA strand breaks, the non-covalent stabilization of unusual, non-B DNA structures is currently emerging as a promising way to cause DNA damage with a high level of specificity. One of such non-B DNA structures is the three-way DNA junction: this Y-shaped multi-stranded architecture may act as an impediment to many DNA transactions, being therefore regarded as an invaluable target to create genomic defects that are improperly dealt with by cancer cells only. Herein, we report on a series of cationic azacryptands that make excellent candidates for assessing and harnessing the actual therapeutic potential of three-way DNA junction interacting compounds.