Cell walls are an important and growing subject of research in plant biology. In the last decade, there has been an increasing interest in using cell walls as feedstock for the production of second generation biofuels. This has resulted in an expansion in the number of cell wall studies and has highlighted the need for a better understanding of cell wall structure and function. Cell walls are composed of polymers with complex and dynamic structures that vary between cell types and developmental stages as well as between taxonomic groups of plants. To address the diversity of glycans that form the cell wall, it is important to have tools that image these glycans at the cellular level. Antibodies that recognize specific cell wall components are currently one of the most effective and specific molecular probes available for determining the location and distribution of polymers in plant cell walls in situ. Here, emphasis is given to the use of cell-wall-directed antibodies in the context of bioenergy research and the development of cost-effective strategies and effective bioengineering processes to efficiently deconstruct biomass into fermentable sugars.