Nanopores have emerged as a powerful, label-free technique for single molecule analysis, offering high sensitivity and rapid analysis capabilities. Originally developed for DNA sequencing, nanopores have shown promise not only for the characterization of other biomolecules, such as RNA, proteins, and glycans but also of small inorganic compounds, such as nanoparticles. Glycosaminoglycans (GAGs) are a linear, highly charged subclass of glycans, which play essential roles in cell signaling, tissue development, and inflammation processes. The immense structural complexity of GAGs involving unique sulfation patterns renders their analysis challenging. This chapter provides a comprehensive overview on the application of biological and solid-state nanopores for the analysis of GAGs.