Cleidocranial dysplasia is an autosomal dominant condition caused by mutation of RUNX2, characterized by generalized dysplasia of the bones and teeth. Affected individuals have short stature, atypical facial features, and skeletal anomalies affecting mainly the skull and clavicle. The dental manifestations are mainly delayed exfoliation of the primary teeth and delayed eruption of the permanent teeth, with multiple impacted supernumeraries, and absence of cellular cementum. The frequency of this disorder is 1 per million individuals. Here we report a rare case of CCD in a 9-year-old male patient having most of the characteristic features of this syndrome. Interestingly, disorganized dentinal tubules were found in the roots of an extracted deciduous first molar, which seems to be a unique feature not reported previously.