Two key issues must be addressed in the discussion of targeting leukemic stem cells: (1) can the leukemic stem cell be targeted in vivo, and (2) how to assess whether the leukemic stem cell is actually being targeted. Currently several small molecule and antibody- or ligand-based agents have shown activity in selectively targeting the leukemic stem cell. However, there is debate about how to use these targeted agents and how to identify and quantitate the leukemic stem cell to determine whether or not it is being targeted. Parameters are suggested here to help identify and quantitate leukemic stem cells in the clinical context.