Despite the undisputed modern development of synthetic biomaterials that range from bioactive unresorbable to restorable materials, clinically applied osteoconduction bone substitutes still have limitations in the treatment of bone defects. These are the result of the physical and chemical properties of the utilized materials and the biological interactions associated with both local and general reactions of the organism. Mesenchymal stem cells constitute a promising treatment alternative in orthopedics. Preclinical studies regarding the use of mesenchymal stem cells have shown good therapeutic results. However, it is still necessary to advance further in this area and enable the treatment of patients with critically large bone defects. The aim of this review is to describe the role of mesenchymal stem cells in bone repair and regeneration, describe the techniques used in the clinical application of mesenchymal stem cells and outline future research endeavors in this area.