Mesenchymal stem cell (MSC) immunosuppressive properties offer a potentially attractive therapeutic modality for autoimmune diseases. MSC inhibit virtually all types of immune responses in vitro and prevent the induction of disease in several experimental models of autoimmunity. However, the processes involved in the pathogenesis of human diseases are more complicated and treatment cannot be administered before disease induction. In autoimmune diseases persistent antigenic stimulation recruits endogenous MSC to the site of lesion that contribute to the fibrotic evolution. Therefore, administering MSC to a chronic inflammatory disorder may not be desirable. In fact, MSC are not constitutively immunosuppressive but require a ‘licensing’ step provided by molecules of acute phase inflammation, like IFNγ and TNF-α, or toll-like receptor (TLR) ligands. Conversely, different cytokines and/or the stimulation of selective TLR make MSC to become immunostimulatory. Therefore, dissecting the inflammatory environment in autoimmune diseases will identify the best conditions amenable to successful MSC therapy.