Metabolomics involves the global measurement of small molecule metabolites in a biological system and allows the comprehensive investigation of metabolic pathways in pathogenic parasites. Metabolomics studies have enabled the discovery of novel aspects of parasite metabolism that constitute attractive drug targets, and have elucidated metabolic targets of antiparasitic compounds. This chapter provides an introduction to parasite metabolomics and describes metabolomics methods suitable for kinetoplastid and apicomplexan parasites. Several examples are provided describing applications of metabolomics to understand the mechanisms of action and resistance for a range of antiprotozoal compounds. This unbiased elucidation of drug mechanisms with metabolomics will facilitate the discovery and development of new drugs for parasitic diseases of global importance.