Macrocyclic polyamines comprise a special group of heterocycles that bind different guests. Over the past decade, medical interest has focused on macrocyclic polyamines owning to their chemical and biological properties. The discovery and development of the bicyclam AMD3100 highlighted the clinical potential of such compounds in AIDS, cancer and stem-cell mobilization. Many macrocyclic polyamines and their transition metal complexes had the cytotoxic activities to tumors through binding DNA, cleaving DNA, crosslinking DNA, or depleting the endogenous ATP levels of the tumor cells. Furthermore, macrocyclic polyamines also could be labeled with metal ionic radii and have applications in cancer radioimmunotherapy and in vivo magnetic resonance imaging (MRI). The current rational design, and medical applications of macrocyclic polyamines will be reviewed in this manuscript.