The comprehensive characterisation of complex parameter space in '-omics' technologies requires high-throughput systems. In vitro compartmentalisation of reactions in water-in-oil droplets combines the necessary ability to carry out large numbers of experiments under controlled conditions with quantitative readout, and has recently advanced towards automation by generating droplets in microfluidic devices. Some approaches based on these principles are already familiar (e.g. emulsion PCR for sequencing), others, including directed evolution or cell-based assays, are in advanced stages of development--and proof-of-principle experiments are appearing for a whole range of applications in diagnostics, cellomics, proteomics, drug discovery and systems and synthetic biology. This review describes the current state-of-the-art, notes salient features of successful experiments and extrapolates in the direction of more highly integrated systems.