Plant cell walls define cell shape during development and are composed of interlaced carbohydrate and protein networks. Fluorescent dyes have long been used to label plant cell walls, enabling optical microscopy-based interrogation of cell wall structure and composition. However, the specific cell wall components to which these dyes bind are often poorly defined. The availability of fluorescent compound libraries provides the potential to screen for and identify new fluorescent compounds that interact with specific plant cell wall components, enabling the study of cell wall architecture in intact, living tissues. Here, we describe a technique for screening fluorescent compound libraries for enhanced fluorescence upon interaction with plant cell walls, a secondary screening method to identify which cell wall components interact with a given dye, and a protocol for staining and observing Arabidopsis seedlings using a fluorescent cell wall-labeling dye. These methods have the potential to be applied to screening for differences in cell wall structure and composition among genetically diverse plant varieties or species. © Springer Science+Business Media New York 2014.