Recent research data on chondroitin sulfate have suggested that they have many new biological functions such as anti-atherogenesis, anticoagulation, prevention and cure of arthritis, protection and repair of neuron during CNS development, morphogenesis and cell division. They are widely applied to functional food, clinical medicine and biomaterial. However, these bioactivities and applications are dependent on their fine structure with different monosaccharide unit and sulfation patterns. This review provides information on intimate relationship between these biological functions and the structure. Moreover, we overviewed the newly analytical methods about the composition and fine structure of them, including chromatometry, high performance liquid chromatography, mass spectrum and nuclear magnetic resonance before and after enzymolysis.