The subject invention pertains to materials and methods for the prevention and treatment of gastrointestinal diseases, including inflammatory bowel diseases such as Crohn's disease and ulcerative colitis. Therapeutic compositions of the invention include compositions that can neutralize hydrogen peroxide, such as reducing agents and oxidizing agents. In one embodiment, a therapeutic composition of the invention comprises a reducing agent such as sodium thiosulfate. Therapeutic compositions of the invention can optionally include compounds with antibacterial activity, compositions that inhibit bacterial adherence to cells and tissue, compositions that inhibits epithelial lipid peroxidation, compositions that add viscosity to a solution, compositions that inhibit most cells, and/or compositions that help to seal or repair tight junctions between cells of the colonic epithelium of the gastrointestinal tract. Methods of the invention include administration of compounds or compositions of the invention. In one embodiment, compounds or compositions of the invention are rectally instilled in a patient.