It is becoming clear that variations in inflammatory response are a major determinant in susceptibility to periodontitis. However, our understanding of the relationship of the causal agents in periodontitis to the pathogenesis is not as clear as we once thought, and thus therapies based on etiopathogenesis are similarly in question. We are entering a new era of therapeutic discovery that may have a major impact on our management of the periodontal diseases. Fundamentally, periodontitis is an irreversible condition and once both soft and hard tissues are lost, the healthy periodontal architecture cannot be completely or predictably rebuilt. The discovery of new families of lipid mediators of resolution of inflammation (the lipoxins) and eicosapentaenoic-acid- and docosahexaenoic-acid-derived chemical mediators (the resolvins and protectins) opens new avenues to designing resolution-targeted therapies to control the unwanted side effects of excessive inflammation. The novel protective and therapeutic actions of pro-resolution lipid mediators following microbial challenge are mediated by regulation of the local and systemic inflammatory response that has a direct impact on the organization of the biofilm (plaque) and suggests a new paradigm in clinical periodontal therapeutics.