High throughput (HT) screening is at the starting point for most drug discovery programs. As the range of targets being pursued widens new technologies have to be deployed to enable assays built to measure the activity of proteins previously deemed challenging. Flow cytometry is a technology providing multi-parametric analysis of single cells or other particles in suspension, such as beads. High throughput (HT) flow cytometry has become a very attractive screening platform for drug discovery. In this chapter we describe a 1536 well format high throughput screen of 500,000 compounds to find inhibitors of Rac1 GTPase to prevent allergic airway hyper-responsiveness in asthma. We discuss the assay development, miniaturization and validation carried out prior to the full screening campaign. We then describe how we have automated our iQue® HD screener instruments and how we proceed with the data analysis and explain why we chose to run this screen on a flow cytometer and how it enabled us to reduce cost and timelines for the project.