Objective: The purpose of this study was to evaluate the effect of cavity preparation using hand instruments and conventional rotary instruments on the bonding of glass-ionomer cements to formerly carious teeth. Method and Materials: In 2 experimental groups (12 teeth each with primary caries) caries was removed and cavities prepared using hand instruments according to the atraumatic restorative treatment (ART) technique or conventional rotary instruments. In the control group (12 caries-free teeth) Class 1 cavities were prepared using conventional instrumentation. Cavities in all teeth were restored with 1 of the commercial glass-ionomer cements designed for use with the ART technique, either Fuji IX (GC) or Ketac Molar (3M Espe). After 21 days of storage in physiologic saline at 37°C, 3 400-µm-thick slices from each tooth were stained using the Mallory method and evaluated using a light transmitting microscope. Results: In all samples, a region of interaction was observed between the cement and dentin and enamel. However, the interface in teeth from which caries had been removed was different from that in the control group. All were stained using Mallory staining, but only teeth which had been carious showed coloration. No differences were found in intensity of color or appearance between the cavity preparation techniques. Conclusion: The occurrence of caries in a tooth alters the bonding behavior of glass ionomers to that tooth. The method of caries removal (ART or conventional preparation) does not influence the quality of the interface between a glass ionomer and either dentin or enamel. Keywords: atraumatic restorative treatment (ART), bonding, glass-ionomer cement, interfaces, tooth preparation