Glycosaminoglycans (GAGs) are linear polysaccharides having disaccharide building blocks consisting of an amino sugar (N-acetylglucosamine, or N-acetylgalactosamine) and a uronic acid (glucuronic acid or iduronic acid) or galactose. Glycosaminoglycans have sulfated residues at various positions except for hyaluronan, and those sulfated residues regulate the biological functions of a wide variety of proteins, primarily through high-affinity interactions mediated by specific patterns/densities of sulfation and sugar sequences. Alteration of GAG structure is associated with a number of disease conditions and therefore the analyses of GAG structures and their sulfation patterns are important for the development of disease biomarkers and for treatment options. Extensive structural and quantitative analyses of GAGs from human blood are largely unexplored which may be due to the exhaustive isolation process because of the presence of too much interfering proteins and lipids such as serum albumin. Therefore we established a new GAG isolation method using the least amount (~200 μl) of human blood, consisting of a combination of proteolytic digestion and selective ethanol precipitation of GAGs, digestion of GAGs recovered on the filter cup by direct addition of GAG lyase reaction solution, and subsequent high-pressure liquid chromatography of unsaturated disaccharide products that enable to analyze GAG structures and contents. This isolation method offers an 80 % recovery of GAGs and can be applied to analyze a minute GAG content (≥1 nmol) from the least amount of biological fluids. Hence the method could be useful for the development of disease biomarkers.