Methods for removing endotoxin from naturally occurring materials, such as polysaccharides (e.g., agarose and/or carrageenan) are described herein. Polysaccharides that are substantially free of endotoxins and uses thereof are also described. The polysaccharide materials can be isolated from microorganisms, multicellular organisms, such as, algae, plants, seaweed, etc. The method involves the use of acidic and basic solutions to hydrolyze the lipid-polysaccharide bond in endotoxins. Cleaving the fatty acid from the polysaccharide reduces the water-solubility of the fatty acid and enables its removal with an organic solvent such as ethanol. The polysaccharide component can also undergo acidic or basic hydrolysis due to the weak glycosidic bond between the sugar rings.