Publisher Summary Most biological processes involve specific protein–protein interactions. The yeast two-hybrid system represents a powerful in vivo approach to analyze interactions among macromolecules and screen for polypeptides that bind to a given bait protein. Bacterial equivalents to the yeast two-hybrid system have not been developed yet. This chapter describes a novel bacterial two-hybrid system that allows an easy in vivo screening and selection of functional interactions between two proteins. This system, because of its sensitivity and simplicity, could have broad application in the studies of structure–function relationships in biological macromolecules, in the functional analysis of genomes, and in high-throughput screening of interacting ligands or new therapeutic agents.