Mesenchymal stromal cells (MSCs) are being employed in clinical trials to facilitate engraftment and to treat steroid-resistant acute graft-versus-host disease after hematopoietic stem cell transplantation, as well as to repair tissue damage in inflammatory/degenerative disorders, in particular, in inflammatory bowel diseases (IBDs). When entering the clinical arena, a few potential risks of MSC therapy have to be taken into account: (i) immunogenicity of the cells, (ii) biosafety of medium components, (iii) risk of ectopic tissue formation, and (iv) potential in vitro transformation of the cells during expansion. This paper analyzes the main risks connected with the use of MSCs in cellular therapy approaches, and reports on some of the most intriguing findings on the use of MSCs in the context of regenerative medicine. Experimental studies in animal models and phase I/II clinical trials on the use of MSCs for the treatment of IBDs and other inflammatory/degenerative conditions are reviewed.