Methods, compositions and kits are provided for enhancing remineralization of a tooth or bone containing hydroxyapatite and inhibiting caries progression or loss of hydroxyapatite using a bisphosphonate or pyrophosphonate. The tooth or tooth surface contains a trauma or defect, for example the tooth contains a caries that is identified using a detectable probe. The bisphosphonate or pyrophosphonate is contacted to the tooth and/or oral cavity and binds to the hydroxyapatite material in the tooth or bone and prevents loss of hydroxyapatite material or strengthens the hydroxyapatite. The amount and extent of enhanced remineralization or of inhibition of caries progression and loss of hydroxyapatite are determined by techniques including photography, light microscopy and fluorescence microscopy.