Cellular responses often involve a transition of cells from one state to another. A transition from a stem cell to a differentiated cell state, for example, might occur in response to gene expression changes induced by a transcription factor, or to signaling cascades triggered by a hormone or pathogen. Regulatory networks are thought to control such cellular transitions. Thus, many researchers are interested in reconstructing regulatory networks, not only with the aim of gaining a deeper understanding of cellular transitions, but also of using networks to predict and potentially manipulate cellular transitions and outcomes. In this review, we highlight approaches to the reconstruction of regulatory networks underlying cellular transitions, with special attention to transcriptional regulatory networks. We describe recent regulatory network reconstructions in a variety of organisms, and discuss the success they share in identifying new regulatory components, shared relationships and phenotypic outcomes.