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Atomic force microscopy (AFM) studies have revealed 30–40 nm-wide regular positively charged bands across maturation-stage rat enamel crystals. Low pH resolved these into positively charged spherical domains of ≈ 30 nm diameter. Crystal surface pK values from adhesion force titrations were ≈ 6.5. The effect of fluoride on this pK value and on the nanostructure of fluorosed human enamel crystals has not been reported. The nanostructure and surface chemistry (pK) of normal and fluorotic human and of fluoride-treated rat maturing enamel crystals was examined. Enamel was sectioned and polished, prior to examination, using AFM in height and friction modes. High-resolution height images revealed 30 nm-diameter spherical domains within crystals, arranged as layers of hexagons or as a shallow spiral. Fluorotic enamel showed similar, but less well ordered, nanodomains. These could represent an arrangement of original initiation sites or binding sites for modulating matrix proteins. Surface pK was derived from adhesion-force measurements between functionalized tips (OH or COOH) and crystal surfaces between pH 2 and pH 10. pK values of ≈ 6.5 for normal crystals were reduced to ≈ 5.5 after fluoride treatment. Reduction in surface pK by fluoride might indicate lowered protonation with possible effects on matrix protein binding.