The present invention provides devices, systems and methods for orthodontic treatment using elastic repositioning appliances while concurrently providing dental and periodontal therapies. The appliance (10) comprises a polymeric shell (12) having cavities (14) shaped to receive and resiliently reposition teeth from one tooth arrangement to a successive tooth arrangement. The polymeric shell may include a layer of agent (15), an agent gel or putty (22), a controlled release sheet (25) or reservoirs (60) for holding and dispensing therapeutic agents during orthodontic treatment.