Choanal atresia (CA) results from the developmental failure of the posterior nasal cavity to communicate with the nasopharynx. Computed tomographic (CT) scanning is often used as a diagnostic tool for CA as it is able to provide information regarding the extent and type of atresia. Studies have used CT measurements to analyze the skeletal deformities of children with CA. Computed tomographic analysis of the complete craniofacial skeletal characteristics of children with CA has not been previously reported. This study analyzed the craniofacial skeletal characteristics of infants with bilateral choanal atresia (BCA) and compared them with age-matched standards. Eight patients with BCA under the age of 3 months were evaluated. Fourteen cranio-orbitozygomatic variables were used to represent the craniofacial skeletal configuration. The measurements from the control group were compared with the available values of age-matched normal controls. Statistically significant differences between the means of the sample group and control group were demonstrated in 10 of 14 variables. The sample group means were consistently smaller than the control group mean. Detailed knowledge of the underlying anatomy of infants with BCA will help in the development of treatment strategies and will provide data for evaluation of operative intervention on craniofacial growth.