A histopathological and analytical study of a permanent tooth from a patient with cleidocranial dysostosis (CCD) was performed. The patient was a 47-year-old woman, who had 10 erupted permanent teeth and 2 partially erupted and 19 completely impacted teeth, including supernumerary teeth. The erupted right upper premolar was extracted and observed using a light microscope and an electron probe X-ray microanalyzer (EPMA). Findings showed enamel hypoplasia, predominantly irregular globular dentin and Tomes' granular layer, and a complete lack of cellular cementum in the ground section. The incremental von Ebner and counter Owen lines were obscure. Comparative quantitative analysis using the EPMA showed that the quantities of calcium and phosphate were lower in the enamel and dentin than those of the control sample.