The regeneration of damaged cartilage in different pathological situations is a major goal for the future and could be achieved through cell and/or gene therapy. Mesenchymal stem cells (MSCs) are the progenitors of multiple lineages, including bone, cartilage, muscle, fat, and astrocytes. MSCs seem to be the best candidates for cell therapy to regenerate injured tissue, as they are easily isolated from bone marrow and can be rapidly amplified. Full healing is extremely demanding, however, and includes integration of the regenerated tissue within the surrounding host tissue and true differentiation through pathways involved in embryonic development. This goal might be reached through the combined use of scaffolds, MSC-mediated therapy and the expression of selective differentiating factors. The long-term behavior of MSCs associated with biomaterials and implanted in pathological joints remains to be investigated before clinical application in osteoarthritis or rheumatoid arthritis.