The combination of microfluidic manipulation of emulsion droplets and in vitro compartmentalization offers a means to parallelize biological and chemical assays in droplets. These droplets behave as independent microreactors that are produced, actuated and analyzed at rates of the order of 1000 droplets per seconds providing tools to parallelize assays on small volumes (pL to nL range) for high-throughput -screening: the throughput of the assays performed in droplets is 1000 times larger than the throughput of existing technologies, based on micromanipulation of liquid in microtitre plates by robotic devices. The droplet-based microfluidic technology enables controlled manipulation, analysis and sorting of cells, genes and macromolecules based on their enzymatic activities, as well as chemical compounds based on their activity on biological targets. The integration of microfluidic systems for a series of complex individual operations on droplets could offer a solution to the miniaturization and automation of biological assays, combined with a decrease of the assay volumes and an increase of throughput, going beyond the capacities of conventional screening systems.