Atomic force microscopy (AFM) was used to comparatively study the structure of the bone matrix of rat tibia from an intact region with that from regions submitted to surgical injury. We used young male adult rats (Wistar), with corporal masses between 250 and 300 g. Each injury was provoked by drilling a 1.5-mm-diam hole in one cortical tibia surface. The healing course was monitored at 8 and 15 days after the injury. Atomic force microscopy images, at different magnifications, allowed the identification of the time dependence of the osteoblast activity, measured by the increase in the area of neoformed primary bone and in the organization of the collagen fibers of the bone matrix. Characterization of the natural recovery of the damaged bone tissue by AFM is potentially of great importance because it allows the comparison of natural recovery processes with those induced by medicines and other therapeutic procedures.