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Caries Detector staining reveals 4 zones in dentin containing caries lesions, but characteristics of each zone are not well-defined. We therefore investigated the physical and microstructural properties of carious dentin in the 4 different zones to determine important differences revealed by Caries Detector staining. Six arrested dentin caries lesions and 2 normal controls were Caries-Detector-stained, each zone (pink, light pink, transparent, apparently normal) being analyzed by atomic force microscopy (AFM) imaging for microstructure, by AFM nano-indentation for mechanical properties, and by transverse digital microradiography (TMR) for mineral content. Microstructure changes, and nanomechanical properties and mineral content significantly decreased across zones. Hydrated elastic modulus and mineral content from normal dentin to pink Caries-Detector-stained dentin ranged from 19.5 [10.6–25.3] GPa to 1.6 [0.0–5.0] GPa and from 42.9 [39.8–44.6] vol% to 12.4 [9.1–14.2] vol%, respectively. Even the most demineralized pink zone contained considerable residual mineral.