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Polysialic acid (polySia) is a highly anionic polymer of sialic acid that mostly modifies the neural cell adhesion molecule (NCAM), and involved in brain functions such as learning, memory, circadian rhythm, and social behaviors, through making repulsive and attractive fields on the cell surface. Recently, polySia has been reported to have relationships with some diseases such as psychiatric disorders and cancers. To understand functions of polySia and to apply evaluation methods of polySia structures to the diagnosis of diseases, the comparison of the methods for determining the quality and quantity of polySia structures would be important and necessary. In this study, two monoclonal antibodies, 12E3 and 735, of distinct binding properties were chosen for immunochemical methods by an enzyme-linked immunosorbent assay (ELISA) and a Western-blotting. Two chemical methods, mild acid hydrolysis-fluorometric anion exchange chromatography (MH-FAEC) analysis, and fluorometric C7 /C9 analysis were also chosen. These methods were applied to a small amount of crude adult and embryonic brain homogenates to evaluate the quantity and quality of polySia structure. The quantity of polySia can be evaluated using anti-polySia antibodies by ELISA. In addition, MH-FAEC can be also applied to the evaluation of both quantity and quality (chain length) of polySia chain. Biochemical characters of polySia-NCAM in crude homogenates can be analyzed using a mono Q-anion exchange chromatography. Combinational analyses of these methods could help our further understanding of polySia structure, and the quantity and quality of polySia will become criteria useful for diagnosis of diseases.