For many stem cell experiments, especially those with therapeutic applications, it is important to culture embryonic stem (ES) cells under defined conditions in order to reduce experimental variability. The addition of small molecules to ES cell culture media can aid in the optimization of ES cell survival, proliferation, and maintenance of pluripotency. Under certain conditions, the use of bioactive small molecules may serve as a substitute for undefined culture media. The undifferentiated and pluripotent state of ES cells can be enhanced by activation of the Wnt signaling pathway and by the addition of indole derivatives, such as ID 8. In addition, Tocris biochemicals and compounds can be used to induce the differentiation of ES cells into specialized cell types. For example, alkyl hydrazone derivatives, such as IDE-1, can activate TGF-beta signaling and induce the differentiation of ES cells into definitive endoderm.