Objective: To determine the effects of vitamin D receptor (VDR) deficiency on mouse dentin and enamel mineralisation, and how normalisation of serum calcium level affects dentin and enamel phenotypes in VDR knockout mice. Materials and methods: Groups of VDR wild-type (VDR+/+), VDR deficient (VDR-/-) and VDR-/- rescued mice were sacrificed at 70.5 days of life. The rescued group was established by a high-calcium diet feeding the VDR-/- mice from postnatal 19 days. Micro-CT was used to compare enamel and dentin mineralisation density (MD) at different levels of mandibular incisors among the groups. The scanning electron microscope (SEM) was used to examine the ultrastructure of the enamel and dentin in the corresponding levels and of surface enamel after acidic treatment. Results: Micro-CT showed that in VDR-/- rescued group, dentin phenotype was reversed and dentin MD was reversed to normal; however, enamel mineralisation was not reversible, and remained as hypermineralisation in molar region and apical region of the incisors. SEM also revealed enamel hypermineralisation in the VDR-/- rescued group. This early enamel hypermineralisation was more susceptible to acidic erosion. Conclusion: Vitamin D affects dentin mineralisation systemically, and it regulates enamel mineralisation locally.