Background. Using different software to evaluate the airways, with different thresholds, but within the range for airway recognition, could yield different measurements in the same patient with or without craniofacial disharmony. Objectives. The aim of the present study was to compare the volume and the most constricted area (MCA) of the oropharynx in individuals with or without an open bite by using 2 software programs meant for cone-beam computed tomography (CBCT). Material and methods. This comparative study included 60 cases selected from 137 CBCT scans obtained from individuals with the presence or absence of an open bite. Each group included adults of both genders – in total 30 women and 30 men – with a mean age of 27.57 ±11.85 years in the open bite group and 26.23 ±6.78 years in the control group. The oropharyngeal volume and MCA were measured with 2 three-dimensional (3D) software packages: Planmeca Romexis®; and Nemotec NemoStudio®. Two calibrated orthodontists trained in the use of the software made the measurements. Data was analyzed using Student’s t tests for independent and paired samples (p < 0.05). Results. In general, the oropharynx volume measurements obtained with the NemoStudio software were significantly higher than those obtained with Romexis (19,007.17 ±8005.79 mm3 and 17,823.47 ±7148.62 mm3, respectively) (p = 0.020). However, when the groups were analyzed sepa-rately, the measurements of the group with an open bite did not differ according to the software used (p = 0.352). The measurements of the MCA of the oropharynx were significantly higher when obtained with the NemoStudio software (MD (mean difference) = 19.02 mm2) (p = 0.005). In contrast, no difference in the MCA results for the 2 software packages was found in the open bite group (p = 0.728). Conclusions. The volumetric and cross-sectional measurements of the oropharyngeal airway, particularly in individuals without an open bite, were affected by the software used.