Summary We describe here a methodology that enables the occurrence of cell‐wall glycans to be systematically mapped throughout plants in a semi‐quantitative high‐throughput fashion. The technique (comprehensive microarray polymer profiling, or CoMPP) integrates the sequential extraction of glycans from multiple organs or tissues with the generation of microarrays, which are probed with monoclonal antibodies (mAbs) or carbohydrate‐binding modules (CBMs) with specificities for cell‐wall components. The profiles generated provide a global snapshot of cell‐wall composition, and also allow comparative analysis of mutant and wild‐type plants, as demonstrated here for the Arabidopsis thaliana mutants fra8 , mur1 and mur3 . CoMPP was also applied to Physcomitrella patens cell walls and was validated by carbohydrate linkage analysis. These data provide new insights into the structure and functions of plant cell walls, and demonstrate the potential of CoMPP as a component of systems‐based approaches to cell‐wall biology.