In clinical practice, dentists must frequently bond adhesives to caries-affected dentin substrates, but the bond that characteristically forms with these substrates does not provide the durability necessary for long-term clinical function. The purpose of this study was to characterize and compare the interfacial chemistry of adhesive with caries-affected and noncarious dentin using micro-Raman spectroscopy. The results indicated that the differences in the Raman spectra between noncarious and caries-affected dentin could not be accounted for by simple decreased mineralization. Both the structure of collagen and mineral in the caries-affected dentin has been altered by the caries process. The differences in structure and composition not only interfered with acid-etching process but also subsequent resin monomer penetration. It was shown that the interface between the adhesive and caries-affected dentin was wider and more complicated than that of the adhesive and noncarious dentin. As a result of adhesive phase separation, a structurally integrated hybrid layer did not form at the interface with either caries-affected or noncarious dentin. Using chemical imaging techniques, this study provides the direct evidence of adhesive phase separation at the interface with caries-affected dentin. Although our group previously reported adhesive phase separation at the interface with noncarious dentin, the chemistry of caries-affected dentin leads to greater variability and a more highly irregular composition along the length and breadth of the interface.