Regulation of immune response was found to play an important role in the course of many diseases such as autoimmune diseases, allergy, malignancy, organ transplantation. The studies on immune regulation focus on the role of regulatory cells (Tregs, Bregs, regulatory myeloid cells) in these disorders. The number and function of Tregs may serve as a marker of disease activity. As in allergy, the depletion of Tregs is observed and the results of allergen-specific immunotherapy could be measured by an increase in the population of IL-10+ regulatory cells. On the basis of the knowledge of anti-cancer immune response regulation, new directions in therapy of tumors are introduced. As the proportion of regulatory cells is increased in the course of neoplasm, the therapeutic action is directed at their inhibition. The depletion of Tregs may be also achieved by an anti-check-point blockade, anti-CD25 agents, and inhibition of regulatory cell recruitment to the tumor site by affecting chemokine pathways. However, the possible favorable role of Tregs in cancer development is considered and the plasticity of immune regulation should be taken into account. The new promising direction of the treatment based on regulatory cells is the prevention of transplant rejection. A different way of production and implementation of classic Tregs as well as other cell types such as double-negative cells, Bregs, CD4+ Tr1 cells are tested in ongoing trials. On the basis of the results of current studies, we could show in this review the significance of therapies based on regulatory cells in different disorders.