Bacterial infections, especially those that are resistant to antibiotics, constitute an increasing threat to public health. Deeper understanding about the systems that govern resistant infections, followed by the design of new therapies is crucial to minimizing morbidity and mortality due to antibacterial resistance. To this end, the discovery of small molecules capable of modulating bacterial processes is an important goal. Herein, we summarize recent developments in high-throughput screening, including the use of in vitro biochemical assays, reporter fusion read-out methods, and live cell phenotypic assays in bacteria. We also highlight key advantages and disadvantages of each assay type, as well as exciting new innovations.