Periodontitis is a chronic inflammatory disease leading to alveolar bone destruction, and eventually tooth loss. In genetically or environmentally predisposed individuals periodontopathogenic bacteria trigger an inflammatory immune response where activated macrophages secrete inflammatory cytokines and T helper 17 cells produce interleukin-17, receptor activator of nuclear factor kappa B ligand (RANKL) and tumor necrosis factor-α. Inflammation and the production of RANKL, the key cytokine responsible for osteoclast activation, cause excessive activation of osteoclasts. This results in a decoupling between bone formation and resorption, leading to bone loss. As conventional treatment does not target the inflammatory response and osteoclast activation, its effectiveness is limited. Novel treatments are thus required if we are to cure this disease. Mesenchymal stem cells (MSCs), including those of dental origin, are potent immunomodulators and are known to be suitable for tissue regeneration. MSCs can inhibit the immune response by suppressing T cells, inducing regulatory T cells and converting dendritic cells and macrophages into a regulatory phenotype. Additionally, genetic modulation may enhance the therapeutic potential of MSCs. In the present review the authors describe the potential use of MSCs, either unmodified or engineered for therapeutic purposes in periodontitis, with special emphasis on MSCs from dental pulp and periodontal ligament. The paper envisions that multiple targeting of this inflammatory disease by modulating the immune response, promoting bone regeneration and inhibiting bone resorption might yield significantly improved treatment outcomes when combined with conventional treatment modalities.