Mesenchymal stem cells (MSCs) are multipotent progenitor cells isolated by various relatively easily accessible tissues, such as bone marrow and cord blood. MSCs gained attention because of their ease for in vitro expansion together with their multilineage potential. More recently, in vitro and in vivo immunosuppressive properties have been ascribed to them, as they are able to modulate the function of all major immune cell populations, thus impeding immune responses. The underlying mechanisms of their differentiation and function are not thoroughly understood, but still they represent important candidates for tissue regeneration and manipulation of the immune response in graft rejection, graft versus host disease, and autoimmune disorders. Characteristics and immunogenic profile of MSCs, their interface with immune system and their potential use as immunosuppressive elements in cellular therapeutic protocols are reviewed in this chapter.