Understanding the development of an organ requires knowledge of gene, protein, and metabolite expression in the specific cell types and tissues that comprise the organ. Fluorescence-activated cell sorting (FACS) is an efficient method to isolate specific cells of interest, and the information gained from this approach has been integral to plant developmental biology. The Benfey lab has developed this method to examine gene expression profiles of different cell types in the Arabidopsis root under both standard and stress conditions. In addition to gene expression, downstream applications of FACS include proteomic and metabolite analysis. This is a powerful method to examine biological functions of specific cell types and tissues with a systems biology approach.