The marine environment represents a vast resource to discover bioactive molecules with novel modes of action. The stagnation of the pharmaceutical market in terms of newly approved drugs, along with increased research and development costs, have created an urgent need to accelerate the discovery of new natural chemical scaffolds, and high-throughput screening (HTS) can be used for this purpose. The HTS process involves testing compounds in high numbers, to determine if they can modulate a given molecular pathway. Various HTS assays have been developed, depending on the therapeutic targets. In this chapter, an overview is provided of HTS procedures, and examples given that highlight the potential of marine products as pharmaceuticals, such as inhibitors of protein kinases.