Proteoglycans contain a unique carbohydrate component, glycosaminoglycan, which consists of repeating, typically sulfated disaccharides, and is capable of interacting with diverse molecules. Specific, clustered arrangements of sulfate on the glycosaminoglycan backbone form binding sites for many biologically important ligands such as extracellular matrix molecules and growth factors. Core proteins of proteoglycans also show molecular interactions necessary for organizing scaffolds in the extracellular matrix or for anchoring proteoglycans to the plasma membrane. Experimental protocols aiming at extracting maximal amounts of proteoglycans from tissues or cells require disruption of molecular interactions involving proteoglycans by denaturing solvents. Among many of the proteoglycan separation procedures, anion exchange chromatography, which takes advantage of the presence of highly negatively charged glycosaminoglycans in all proteoglycans, serves one of the most convenient general separation techniques.