The importance of therapeutic use of mesenchymal stem cells is outlined through their immunomodulatory and antiapoptotic effects as well as differentiation potential, which all contribute to faster regeneration. For successful therapeutic use the knowledge about isolation of mesenchymal stem cells, their characterization, differentiation and preservation is needed. Due to their specific effects different application systems which are adapted to different therapies play an important role. Strengths and weaknesses of biomaterials for different applications are discussed as they can be beneficial because of better control over the cells and their differentiation in an open system. At the end the therapeutic effect of mesenchymal stem cells are presented in the case of osteoarthritis, periodontal disease, skin regeneration, chronical wounds, chronic bowel disease and tumor.