A composition having an ionic complex of chitosan and a negatively charged polysaccharide, selected from the group consisting of heparin, heparan sulfate and dextran sulfate, for use in the treatment of mucositis in a mammalian subject, to a method of preventing or treating mucositis in a mammalian subject, by applying topically a composition having an ionic complex of chitosan and a negatively charged polysaccharide, selected from the group consisting of heparin, heparan sulfate and dextran sulfate. The composition further relates to a pharmaceutical composition for topical administration of an ionic complex of chitosan and heparin.