One of the main problems, not fully resolved in orthopedics yet, is the regeneration of large bone defects. The intricate bone composition makes the healing process very complex when dealing with extensive lesions. Although traditional therapeutic approaches allowed significant progresses by proposing new bone substitutes and prosthetic devices, the obtained results remain questionable. To regenerate the bone tissue, tissue engineering focused on the use of mesenchymal cells derived from the bone marrow, in the attempt to restore an environment more suitable for the restitutio ad integrum of the tissue. This chapter describes and discusses the tissue engineering approach in bone repair with particular regard to the new investigative tools developed in recent years to monitor the process.