Mesenchymal stem cells (MSCs) are undifferentiated multipotent cells which reside in various human tissues and have the potential to differentiate into osteoblasts, chondrocytes, adipocytes, fibroblasts and other tissues of mesenchymal origin. In the human body they could be regarded as readily available reservoirs of reparative cells capable to mobilize, proliferate and differentiate to the appropriate cell type in response to certain signals. These properties have triggered a variety of MSC-based therapies for pathologies including nonunions, osteogenesis imperfecta, cartilage damage and myocardial infarction. The outcome of these approaches is influenced by the methodologies and materials used during the cycle from the isolation of MSCs to their re-implantation. This review article focuses on the pathways that are followed from the isolation of MSCs, expansion and implantation.