Stem cells represent a vital component of the body's natural repair mechanisms, providing support for tissues with differentiating cells and responding to regenerative requests in damaged areas. Mesenchymal stem cells are additionally known for their immunomodulatory properties. The immunomodulatory properties of these cells are used in clinical practice for the treatment of immune-associated dysregulations. Mesenchymal stem cells and their derivatives are applied in organ and hematopoietic stem cell transplantation procedures for the treatment of autoimmune disorders and other conditions. Recently immune privileges for them and few other stem cells were demonstrated. Existence of stem cells immune privileges was reasoned by cross action between processes of regeneration and inflammation and as a part of peripheral control of autoimmunity. A new fundamental feature of stem cells requires integration into the general understanding of evolution and regulation of the stem system. I suggest a functional model which links the attributes of stem cells, including quiescence, response to regeneration request, immune modulation, and the maintenance of homeostatic differences, as well as their low percentage in tissues. I suggest that immune modulating stem cells (IMSCs) should be recognized as a relevant part of the immune system.