The plant cell wall is an extracellular matrix, which can be viewed as a multifunctional subcellular compartment involving many fields of research: growth and development, plant-pathogen interactions, stress, cell-to-cell signaling, metabolic processes, biomaterials and biofuels, and many others. Given its importance, much of the research effort has been directed toward investigating the plant cell walls containing plant cell wall proteins, which are essential constituents of plant cell walls and play essential roles in many biological processes, and yet there is still not a distinct repertoire of the plant cell wall proteins. Several functional screen procedures including a yeast secretion trap, an Agrobacterium-mediated transient expression assay and a subcellular localization study, have been recently optimised to confirm secretion and localization of an ever-growing list of plant cell wall proteins. These functional screen approaches collectively provide a powerful suite of means to identify and characterize a dynamic and complex plant cell wall proteome. Thus, the potential outcomes of plant cell wall functional genomics will enable plant breeding programs to develop new strategies for improvement of crop quality.