Our understanding of the biology of Toxoplasma gondii has benefited greatly from the availability of an extensive set of molecular genetic tools to manipulate the parasite, including methods for random and targeted integration of exogenous DNA, gene knockouts, conditional gene expression, and chemical and insertional mutagenesis (see chapter by Striepen, Soldati-Favre and Meissner, this volume). Furthermore, excellent bioinformatics resources for genomic, transcriptomic and proteomic analysis are available (see chapters by Roos and Wastling, this volume). Recent advances in the use of small molecules to study parasites have established chemical biology as another powerful tool in this toolbox, one that is highly complementary to molecular genetics and bioinformatics. “Chemical biology” is a relatively new term used to describe an experimental approach that shares many techniques and methods with what has traditionally been called pharmacology. However, chemical biology uses small organic molecules not only to induce cellular phenotypes, but also as tools to define and explore biological mechanisms. The emergence of chemical biology as a powerful new experimental approach has been made possible by recent technical advances in organic synthesis, analytical biochemistry, fluorescence microscopy, genomics and proteomics. In this chapter, we will provide an introduction to the field of chemical biology, with a focus on two strategies: forward and reverse chemical genetics. We will compare different methods for identifying the target(s) of bioactive small molecules of interest, and we will describe approaches to target validation and demonstration of compound specificity. We will then provide a few selected examples of how chemical biology has been used to reveal insights into the complex biology of T. gondii and the mechanisms underlying host-parasite interaction. Since chemical biology uses small molecules as the primary experimental tool for mapping biological pathways, the approach necessarily focuses our attention on pathways and targets that are likely to be susceptible to small-molecule perturbation, with potential implications for drug development.