Dentin conditioners provide a microporous surface for penetration by bonding agents. This study used an atomic force microscope (AFM) to examine the initial steps in the conditioning process of dentin using three demineralizing agents, 0.5 M EDTA, and dilute solutions of phosphoric (3 mM, 6 mM) and citric (5 mM) acids, in order to establish the relationships between demineralization and changes in surface morphology. Polished dentin disks had a 10-nm-thick gold pattern applied which served as a height reference. Samples (n = 3/agent) were examined at baseline and at 2-s intervals for up to 120 s for each agent. EDTA (0.5 M) was used as received; other conditioners were diluted to slow the rates of demineralization for detailed study. The surfaces of the peritubular and intertubular regions were al- tered differently. Initially subsidence rates were equal and linear, but after a 100-nm depth change the intertubular rates decreased. For phosphoric acid and citric acid, the movement of the intertubular surface was uniform and the surfaces remained smooth. However, the intertubular surfaces were rough for the EDTA treatment. The surface subsidence reached a plateau after a depth change of about 0.5 pm, which resulted from a limit to the contraction of the demineralized and hydrated collagen scaffold.