Impairment of immunological reactivity in inflammatory periodontal diseases is well proven. To perform immunomodulatory treatment in domestic dental practice, various medications are used, including natural, chemically modified, recombinant, genetically engineered and synthetic substances, which differ in their effects upon innate and adaptive immune systems. Complex preparations of natural cytokines as well as genetically engineered preparations of IL-1, IL-2, growth factors, IFNα, IFNβ, IFNγ are applied in clinical settings. Clinical implementation of interferon and interferon inducers in combined therapy of generalized periodontitis is shown to increase resistance to viral components of the oral microbiota. Growth factors (platelet growth factor, fibroblast growth factor, endothelial growth factor, etc.) are successfully used for tissue regeneration in periodontics and maxillofacial surgery. Experimental studies have shown that local administration of toll-like receptor-9 and CD40 ligand may reduce periodontal ligature inflammation and bone loss in mice by inducing B-cell proliferation and increasing IL-10 mRNA expression. Promising results in development of new biologically active drugs are obtained with nanotechnology approaches, i.e., production of composite materials of metal nanoparticles with polymers, growth factors, and local application of these products. General limitations of all these growth factors include extremely short periods of biological activity, and adjusted duration of local effective concentrations. Therefore, it is important to develop a drug delivery system using appropriate scaffolding elements thus allowing local effects of the drug for a certain period of time. In experimental models, alginate hydrogels performed well upon local delivery of granulocyte-macrophage colony-stimulating factor and stromal lymphopoietin of the thymus. A new immunomodulatory strategy for alveolar bone regeneration targets macrophages. A biologically functionalized injectable microsphere of heparin-modified gelatin nanofibers that mimic the architecture of the natural bone extracellular matrix, and provide an osteoconductive microenvironment for bone cells includes IL-4, which has heparin-binding domains. These medications represent a component of a comprehensive treatment schedule, and should be evaluated for immune status before and after therapy. Thus, recent advances in studies of innate and acquired immune responses in inflammatory diseases and, in particular, in periodontal disorders, allows us to develop new approaches and methods of treatment in order to improve efficiency of complex therapy in the inflammatory periodontal diseases.