The effect on structural defects of carbonate, zinc, strontium, fluoride and lead inclusions in synthetic apatites has been studied by high resolution transmission electron microscopy. Treatment of dental enamel by zinc and strontium solutions has been similarly investigated. Electron beam damage to crystal surfaces was always seen in unerupted enamel and short-term refluxed aqueous apatites, and occasionally in mature enamel, but was not observed in high temperature synthetic apatites or long-term refluxed aqueous apatites. Concentrated areas of calcium deficiency (15–40 Å in diameter), probably related to screw dislocations, were observed in untreated normal dental enamel and all synthetic apatites except high temperature carbonate-free stoichiometric preparations. These deficient regions are related to carbonate inclusion and are important in the susceptibility or resistance of enamel crystals to acid attack during the dental caries process.