The development of a complete organism from a single cell involves extraordinarily complex orchestration of biological processes that vary intricately across space and time. Systems biology seeks to describe how all elements of a biological system interact in order to understand, model and ultimately predict aspects of emergent biological processes. Embryogenesis represents an extraordinary opportunity (and challenge) for the application of systems biology. Systems approaches have already been used successfully to study various aspects of development, from complex intracellular networks to four-dimensional models of organogenesis. Going forward, great advancements and discoveries can be expected from systems approaches applied to embryogenesis and developmental biology.