The human genome contains a unique class of domains, referred to as AT islands, which consist typically of 200-1000 bp long tracts of up to 100% A / T DNA. The significance of AT islands as potential targets for chemotherapeutic intervention stems from two main aspects. First, AT islands are inherently unstable (expandable) minisatellites that are found in various known loci of genomic instability, such as ATrich fragile sites. Second, AT islands are involved in the organization of the genomic DNA on the nuclear matrix by acting as scaffold / matrix attachment regions, S / MARs. DNA duplexes of AT islands are unusually flexible and prone to base unpairing, which are crucial MAR attributes. Various AT islands show high binding affinity for isolated nuclear matrices and associate with the nuclear matrix in the cell. The cellular MAR function of AT islands may differ in cancer and normal cells. The abnormally expanded AT islands in the FRA16B fragile site in leukemic CEM cells act as strong, permanent MARs, while their unexpanded counterparts in normal cells are loop localized. Given their instability and involvement in the remodeling of the nuclear architecture, AT islands may be a factor in cancerous phenotypes. AT islands are preferentially targeted by the extremely potent DNA-alkylating antitumor drugs, bizelesin and U78779. High lethality of lesions in AT islands is consistent with the critical role of MAR domains in DNA replication. The abnormal structure / function of AT islands, such as their expansion and acquired strong MAR properties, may sensitize cancer cells to AT island targeting drugs.