Increasing evidence suggests that four-stranded tetraplex structures spontaneously form under physiological conditions and these alternate DNA structures are likely to form in vivo. Alternate G-quadruplex DNA structures that may form in regulatory elements of oncogenes or G-rich telomere sequences are potential targets for cancer therapy since these sequence-specific structures are proposed to affect gene expression and telomerase activation, respectively. Small molecule compounds that specifically bind tetraplexes may be used to regulate cell cycle progression by modulating promotor activation or disrupting telomere maintenance, important processes of cellular transformation. In this review, we summarize the current research developments and associated patents that bear relevance to understanding the mechanism and clinical application of tetraplex binding molecules as anti-cancer agents.