Compositions for the treatment of periodontitis and methods of use thereof are described. The compositions contain a polymer-iodine complex. The polymer-iodine complex can be suspended in a pharmaceutically acceptable carrier in which the complex is stable and the iodine is stable in its elemental form and/or a combined form (e.g., iodine-iodide complex). In one embodiment, the complex is prepared by the reacting a synthetic or semi-synthetic ionic polymer, with iodine and/or an iodide. The complex will preferably deliver iodine over an extended period of time for example over several days (e.g., at least 3 days, preferably at least 4 days, more preferably at least 5 days, most preferably at least 6 days), preferably at least a week, more preferably at least two weeks. In one embodiment, the polymer-iodine complex forms a gel, alone or by the addition of one or more gelling agents, upon administration into a periodontal pocket. The polymer-iodine complex, or a gel containing the complex can also contain one or more additional active agents and/or pharmaceutically acceptable excipients. The composition is preferably formulated so that it can be administered by injection.