Stem cell self-renewal and differentiation mechanisms are regulated by growth factors, transcription factors, and signal transduction pathways. These molecular mechanisms, such as Wnt and Hedgehog signaling pathways, can be modulated by naturally occurring and synthetic small molecules. For example, compounds can be targeted to a specific protein within a pathway, and the cellular response can often be controlled by subtle changes in compound concentration. Given that many small molecules act on a desired pathway, researchers may enhance stem cell proliferation and direct cell fate decisions by specifically manipulating signal transduction pathways. In addition, feeder-free stem cell culture methods and the use of defined media supplemented with bioactive small molecules may offer more consistency, reduce experimental variability, and open avenues to therapeutic applications.