Chitosan is a natural product having wide range of applications in the food and cosmetic industries. Food and commodity grade chitosan are laden with pyrogens, such as endotoxins and proteins which limit its applicability in the biological and medical arenas, as minute amounts of endotoxins may induce adaptive and innate responses when contacted with mammalian tissue, pharmaceuticals and biomedical devices. Due to chitosan's ability to avidly bind endotoxin and other pyrogens, they are difficult to remove. The present invention is directed to methods for purifying chitosan from shells, food and commodity grade chitosan into ultra-pure, low endotoxin chitosan having biological and medical applicability. Additionally, the present invention is also directed to a method of determining the pyrogenicity of the ultra-pure low endotoxin chitosan.