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Cleidocranial dysplasia (CCD) is a rare autosomal dominant skeletal dysplastic disease associated with mutations in the gene encoding the Runt-related transcription factor 2 (RUNX2). CCD is characterized by hypoplastic clavicles and patent cranial sutures. Management is essential to prevent complications during growth of the patient. Herein, we report a sporadic case of an infant with hypoplastic skull and clavicles at birth, which correlated with clinical findings of CCD. A heterozygous mutation was identified in the RUNX2 gene, which confirmed the diagnosis of CCD.