Carious lesions exhibit a complex structural organization composed of zones of higher and lower mineralization, formed by successive periods of cyclic de- and re-mineralization. A thorough understanding of the lesion morphology is necessary for the development of suitable treatments aiming to repair rather than replace the damaged tissue. This detailed understanding includes the entire lesion down to individual crystallites and nanopores within the natural organization of the crown. A moderate lesion, with surface loss and reaching dentin, and a very early lesion were studied. Scanning small-angle X-ray scattering (SAXS) with a pixel size of 20 × 20 μm2 was used to characterize these lesions, allowing for the identification of distinct zones with varied absorption and scattering behavior, indicative of varied porosity and pore morphology. Despite these differences, the overall orientation and anisotropy of the SAXS signal was unaltered throughout both lesions, indicating that an anisotropic scaffold is still present in the lesion. The finding that crystallite orientation is preserved throughout the lesions facilitates the identification of preventive re-mineralizing strategies with the potential to recreate the original nanostructure.