This chapter aims to give the reader an overview of the application of high throughput techniques to the screening of conditions in the synthesis of potential drug molecules. Statistical methods for the design of experiments are covered as well as the equipment and automation used for both for the screen creation and analysis, including flow reaction optimisation. In addition, applications are outlined, including catalyst screening for key transformations, biotransformation screening, salt screening and solvent screening for material isolation. Finally the chapter includes case studies of the application of this methodology in drug discovery.