Realizing the potential that human embryonic stem cells (hESCs) hold, both for the advancement of biomedical science and the development of new treatments for many human disorders, will be greatly facilitated by the introduction of standardized methods for assessing and altering the biological properties of these cells. The 7-day in vitro alkaline phosphatase colony-forming cell (AP⁺-CFC) assay currently offers the most sensitive and specific method to quantify the frequency of undifferentiated cells present in a culture. In this regard, it is superior to any phenotypic assessment protocol. The AP⁺-CFC assay, thus, provides a valuable tool for monitoring the quality of hESC cultures, and also for evaluating quantitative changes in pluripotent cell numbers following manipulations that may affect the self-renewal and differentiation properties of the treated cells. Two other methods routinely used to evaluate hESC pluripotency involve either culturing the cells under conditions that promote the formation of nonadherent differentiating cell aggregates (termed embryoid bodies), or transplanting the cells into immunodeficient mice to obtain teratomas containing differentiated cells representative of endoderm, mesoderm, and ectoderm lineages.