Tissue and functional regeneration takes place in the body at various stages throughout life. However, bone, cartilage, tendons, blood vessels and cardiac muscle have a limited capacity for self repair and, after injury or disease, the regenerative ability of these adult tissues is often insufficient and leads to nonfunctional scar tissue. In this context, mesenchymal stem cells, which are adult multipotential progenitors of mesoderm cells (osteoblasts, chondrocytes, adipocytes and stroma cells), represent a major hope for tissue-engineered replacement and regenerative medicine. Furthermore, the autologous use of these cells prevents immunological responses against new tissues and the risks of disease transmission from donors, which are both common problems of organ transplantation. While the existence of mesenchymal stem cells is undisputed, many questions remain regarding their self-renewal and capacity to differentiate, their homogenous nature as a cell population throughout the body and their true potential in regenerative medicine. In this article, the proteomics studies carried out to characterize mesenchymal stem cells and to help understand their physiology are reviewed.