Following the "adhesion-decalcification" concept, specific functional monomers possess the capacity to primary chemically interact with hydroxyapatite (HAp). Such ionic bonding with synthetic HAp has been demonstrated for 10-methacryloyloxydecyl dihydrogen phosphate (10-MDP), manifest as self-assembled "nanolayering". In continuation of that basic research this study aimed to explore whether nanolayering also occurs on enamel and dentin when a 10-MDP primer is applied following a common clinical application protocol. Therefore, the interaction of an experimental 10-MDP primer and a control, commercially available, 10-MDP-based primer (Clearfil SE Bond primer (C-SE), Kuraray) with enamel and dentin was characterized by X-ray diffraction (XRD), complemented with transmission electron microscopy interfacial ultrastructural data upon their reaction with enamel and dentin. In addition, XRD was used to study the effect of the concentration of 10-MDP on nanolayering on dentin. Finally, the stability of the nanolayers was determined by measuring the bond strength to enamel and dentin when a photoinitiator was added to the experimental primer or when interfacial polymerization depended solely on the photoinitiator supplied with the subsequently applied adhesive resin. XRD confirmed nanolayering on enamel and dentin, which was significantly greater on dentin than on enamel, and also when the surface was actively rubbed with the primer. Nanolayering was also proportional to the concentration of 10-MDP in the primer. Finally, the experimental primer needed the photoinitiator to obtain a tensile bond strength to dentin comparable with that of the control C-SE primer (which also contains a photoinitiator), but not when bonded to enamel. It is concluded that self-assembled nanolayering occurs on enamel and dentin, even when following a clinically used application protocol. The lower bonding effectiveness of mild self-etch adhesives to enamel should be ascribed in part to a lower chemical reactivity (nanolayering) with enamel HAp.