The discovery of new compounds with antitumor activity has become one of the most important goals in medicinal chemistry. One interesting group of chemotherapeutic agents used in cancer therapy comprises molecules that interact with DNA. Research in this area has revealed a range of DNA-recognizing molecules that act as antitumor agents, including groove binders, alkylating and intercalator compounds. DNA intercalators (molecules that intercalate between DNA base pairs) have attracted particular attention because of their antitumor activity. For example, a number of acridine and anthracycline derivatives are excellent DNA intercalators that are now on the market as chemotherapeutic agents. Commercially available acridine and anthracycline derivatives have been widely studied from a variety of viewpoints, such as physico-chemical properties, structural requirements, synthesis, and biological activity. However, the clinical application of these and other compounds of the same class have encountered problems such as multidrug resistance (MDR) and secondary and/or side effects. These shortcomings have motivated the search for new compounds to be used either in place of, or in conjunction with, the existing compounds. Unfortunately, the results of this search have not met expectations. Most candidate DNA intercalating compounds tested for use as anticancer agents have shown little or no biological activity. Research in this area has not been without benefits, for it has produced much information about the synthesis and antitumor properties of hundreds of compounds tested on diverse tumor cell lines. This review analyzes the structural and biological considerations relevant to the use of some anthraquinone analogues as anticancer agents, with the emphasis on the relationship between structure and activity.