Few studies have reported on the analyses of drugs targeting enriched populations of cancer stem cells (CSCs) as a means for identifying potent anti-CSC agents. This review evaluates recent information on the identification and functions of specific CSC surface markers, with particular emphasis on colorectal cancers and the screening of drugs to eliminate such cells. Many of these CSC markers are found commonly expressed on CSCs from different cancer types as well as embryonic stem cells. These markers are often related to hypoxic activation of the WNT/b-catenin pathway, cyclooxygenase-2/prostaglandin E signalling and their relationship to LGR5. By effectively using drugs that inhibit these pathways to kill the CSC population, or otherwise forcing them out of dormancy into active cell division, cancers should become more susceptible to chemotherapy. Such combinational therapies targeting both CSCs and proliferating tumor cells should greatly improve upon the current basis for treatment.