Introduction: Children with congenital or acquired craniofacial abnormalities exhibit an array of dental abnormalities like supernumerary teeth, failure of permanent teeth eruption, decreased alveolar bone height, etc. These subjects undergo complex corrective surgeries to improve esthetics and functional derangements, predisposing them to risks of obstructive sleep apnea due to airway obstruction. The various corrective or therapeutic procedures done might lead to airway complications in these children. The study designed was for retrospective evaluation and comparison of the nasopharyngeal (NP) characteristics and assessment of the airway volume three-dimensionally in normal vs cleidocranial subjects. Materials and methods: Cone-beam computed tomography (CBCT) scans of nine subjects with cleidocranial dysplasia (CCD) were compared with the control sample, and matched for age and sex. A 3D-DOCTOR software by Able Software Corporation was used to calculate the volumetric measurements. The correlation and differences among the values were assessed using an independent t-test and Pearson analysis. Results: The values of lower airway width, upper adenoid width, McNamara upper pharynx, retroglossal area, and total pharyngeal area were found to be reduced in the cleidocranial subjects. The NP airway volume and total airway volume also significantly decreased. Discussion: Cleidocranial dysplasia (CCD) being a rare genetic disorder, we could find only nine established cases. Hence our study can be called a pilot study but may work to establish a database of any sort of skeletal and dental anomaly with possible specific respiratory characteristics affecting airway.