Glycosaminoglycans (GAGs) are large, polyanionic molecules expressed throughout the body. The GAG heparin, co-released with histamine, is synthesised by and stored exclusively in mast cells, whereas the closely related molecule heparan sulphate is expressed, as part of a proteoglycan, on cell surfaces and throughout tissue matrices. These molecules are increasingly thought to play a role in regulation of the inflammatory response and heparin like molecules are now being seriously considered to hold potential in the treatment of inflammatory diseases such as asthma. Heparin and related molecules have been found to exert anti-inflammatory effects in a wide range of in vitro assays, animal models and in human disease. The anti-inflammatory activities of heparin are independent of the well-established anticoagulant activity of heparin, suggesting that the separation of these properties could yield novel anti-inflammatory drugs, which may be useful in the future treatment of inflammatory diseases.