Cancer stem cells (CSCs) are functionally defined by their ability to self-renew and recapitulate tumors in the ectopic setting. They have been identified in a growing number of human malignancies and their association with poor clinical outcomes has suggested that they are the major factors in dictating clinical outcomes. Moreover, recent studies have demonstrated that CSCs may display other functional attributes, such as drug resistance and invasion and migration, that implicate a broad role in clinical oncology spanning initial tumor formation, relapse following treatment, and disease progression. Although our knowledge regarding the basic biology of CSCs continues to improve, proof that they are clinically relevant is still lacking, and translation of the CSC hypothesis from the laboratory to the clinic is of paramount importance. We will review current evidence supporting the role of CSCs in clinical oncology and discuss potential barriers and strategies in designing trials examining CSC-targeting agents.