Etching is one of the most fundamental steps in the restoration of teeth by adhesion of composite resin in dental clinics. Atomic force microscope (AFM) was used for the in situ observation of the etching process of human enamel, dentin and synthetic hydroxyapatite in the three different acid agents, 2% phosphoric acid, 10% citric acid and 10% polyacrylic acid. To measure the absolute depth from the initial level before etching and to correlate the surface height between the changing AFM images obtained, the depth profiles were recorded with etching time by carrying out the line scan consecutively at the representative place of the observed area. These chronological series of depth profiles enabled us to perform quantitative analysis of etched amount in addition to the surface roughness obtained from relative depth profile within one image. The course of etching process from the dissolution of smear layer, appearance of enamel prizms or dentinal tubules to progress of demineralization could clearly be observed. The depth profile, surface roughness, etching amount, etching rate and smear layer thickness could then be evaluated. The different etching characteristics of three acid agents and the effect of surface roughness produced by different mechanical prepolish were compared and discussed.