The bonding efficacy of dentin adhesive to caries-affected and caries-free dentin was examined by measuring the wall-to-wall polymerization contraction gap width and micro-tensile bond strength. The morphology of the adhesive interface was observed with a Scanning Electron Microscope (SEM). The cavity wall prepared in the caries-affected or the caries-free dentin was conditioned by 0.5 mol/L EDTA and restored with a commercial resin composite (Silux Plus) mediated with a commercial dentin bonding agent (Clearfil Photo Bond) with or without priming of 35 vol% glyceryl mono-methacrylate (GM). In GM priming groups, complete cavity adaptation was observed in all of the specimens of both caries-free and caries-affected dentin. When the GM priming was omitted, contraction gap width in the caries-affected dentin cavity was significantly decreased compared with that in the caries-free dentin cavity. The micro tensile bond strengths of the caries-free dentin without GM priming were significantly lower than those of the other three groups. It was possible to conclude that the efficacy of the dentin bonding system to caries-affected dentin was never inferior to that of the caries-free dentin. The sclerotic dentin is a defense tissue against carious invasion should be preserved. For a resin composite restoration in a caries-affected dentin cavity, it should not be applied with strong acid for the dentin conditioning.