With the emergence of the cancer stem cell hypothesis in leukemia there has been a need to develop the crucial tools and assays to prospectively isolate these cells from other cancers. This review focuses on the latest strategies to prospectively isolate cancer stem cells and also explores some of the caveats of the methodology that has taken hold. Emerging themes in the cancer stem cell field will be explored, including relevance of cell of origin, intraclonal heterogeneity, and how exploiting the unique functional attributes of stemness in the cancer stem cell population can refine approaches to isolate these cells from various malignancies.