Stem cells can produce progenies that constitute an organism or a tissue while replenishing (renewing) themselves. The ability to produce large quantities of stage-specific cells from self-renewing stem cells in a precisely controlled manner makes it possible to dissect out complex interactions among macromolecules along development, such as early brain development at the global level. These cellular differentiation pathways also serve as templates for identifying biological effects of novel or existing chemical compounds. Thus, stem cells find their most powerful use in chemical biology, which may ultimately lead to applications in regenerative medicine.