To date, much of our understanding of dentin bonding has been based on investigations performed on sound, healthy dentin. This is not the substrate generally encountered in clinical practice, rather dentists must frequently bond to caries-affected dentin. Because of the extreme complexity and variability of the caries-affected dentin substrate, conventional characterization techniques do not provide adequate information for defining those factors that impact bond formation. Using Fourier-transform infrared imaging, we characterized the inhomogeneities and compositional differences across the length and breadth of the caries-affected dentin/adhesive interface. Differences in mineral/matrix ratio, crystallinity, and collagen organization were noted in the comparison of caries-affected and healthy dentin. As compared to healthy dentin, there were striking differences in depth of demineralization, adhesive infiltration, and degree of conversion at the interface with caries-affected dentin.