Plant cell walls are complex, multi-macromolecular assemblies of glycans and other molecules for which composition and molecular architectures can vary extensively. Even though the chemistry of cell wall glycans is now well understood, it remains a challenge to comprehend the diversity of glycan configurations and interactions in muro and how these relate to changes in the biological and mechanical properties of cell walls. Here we describe in detail a method called Epitope Detection Chromatography (EDC) for the analysis of cell wall matrix glycan sub-populations and interconnections. The method combines chromatographic separations with the use of glycan-directed monoclonal antibodies (MAbs) as detection tools. The high discrimination capacity and high sensitivity in the detection of glycan structural features (epitopes) provided by the use of established MAbs allows the study of oligosaccharide motifs on sets of cell wall glycans in small amounts of plant materials such as a single organ of Arabidopsis thaliana without the need for extensive purification procedures. EDC is used to dissect the heterogeneity of xyloglucan and pectic rhamnogalacturonan-I sub-populations and their modulations in A. thaliana organs. This article is protected by copyright. All rights reserved.