Pharyngeal airway space (PAS) assessment has been used in the past for a better understanding of orthodontic and surgical outcomes; however, this analysis could be unreliable. Our objective was to evaluate possible changes in the PAS reading in the same patient from their consecutive cone-beam computed tomography (CBCT) scans.We evaluated a total of 27 patients' CBCT scans obtained at 2 time points with the use of a standardized acquisition protocol. The mean age at T0 was 31 years (range 17-62 years) and the follow-up records (T1) were taken after 4-6 months. Dolphin Imaging software was used to measure the volumes of the nasopharynx, oropharynx, and hypopharynx. We also evaluated the craniocervical position with the use of a lateral cephalogram.The variables exhibited high intraclass correlation coefficients (ICCs) when measuring the same CBCT scan twice (T0 and T0). However, The ICC between the measurements performed on the first and second CBCT scans (T0 and T1) showed that the only variable with high reproducibility between the 2 scans was cranial base, with an ICC >0.97. Average differences of 682.1 mm, 2255.3 mm, and 517.4 mm were found for the nasopharynx, oropharynx, and hypopharynx, respectively. Regarding the cephalometric angles, average differences between T0 and T1 scans were 0.6°, 2.7°, and 0.4° for OPT.CVT, OPT.SN, and cranial base, respectively.Different CBCT exams with equal scanning and patient positioning protocols can result in different 3D PAS readings. A more careful interpretation of CBCT volumetric data to achieve adequate conclusions of the clinical outcomes is necessary.