Bacteria use two-component systems to adapt to changes in environmental conditions. In response to deteriorating conditions of growth, certain types of bacteria form spores instead of proceeding with cell division. The formation of spores is controlled by an expanded version of two-component systems called the phosphorelay. The phosphorelay comprises a primary kinase that receives the signal/stimulus and undergoes autophosphorylation, followed by two intermediate messengers that regulate the flow of the phosphoryl group to the ultimate response regulator/transcription factor. Sporulation is initiated when the level of phosphorylation of the transcription factor reaches a critical point. This chapter describes efforts to understand the mechanism of initiation of sporulation at the molecular level using X-ray crystallography as a tool. Structural analyses of individual members, as well as their complexes, provide insight into the mechanism of phosphoryl transfer and the origin of specificity in signal transduction.