Fluorescence-Activated Cell Sorting (FACS) is a powerful tool that enables plant growth and development to be studied at the cellular level. Flow cytometry is used to isolate subpopulations of cells, such as those of specific cell types, or cells at particular developmental stages that have been marked with fluorescent proteins. Transgenic technology has given us the ability to generate plants that express fluorescent proteins, not just constitutively in particular cell types, but also dynamically in response to endogenous or external factors. By processing such transgenic lines with FACS, it is possible to isolate distinct populations of cells in a wide range of likely response states for further analysis. This is particularly useful for investigating biological mechanisms in plants because the control of growth and development is manifest at the cell type level. Furthermore, the specificity of the resulting data enables fine modelling of the transcriptional networks that exert systems-level control of the transcriptome; hence key regulators of responses and processes in the plant can be identified. In this review, the current state of the art for FACS methods in plants is explored by means of case studies of research in which cell sorting allowed us to make significant new discoveries.