Objective: The upper pharyngeal airway spaces (PAS) is gaining popularity due its close correlation to various malocclusions and different orthodontic treatments. The aim of this study was to compare two software programs; In Vivo 5 Anatomage and Planmeca Romexis viewer in measuring the PAS volume and in localizing and calculating its minimum constriction area (MCA). Materials and Methods: InVivo 5 Anatomage software (version 5.3.1) and Planmeca Romexis viewer (version 6.4.2) were used to view and measure the PAS on 15 CBCT scans. The upper limit of the PAS was established by drawing a line extending from the posterior nasal spine to the pharyngeal wall. The lower limit was determined by a line parallel to the upper limit line. The volume and MCA of the PAS were automatically calculated by each software. Measurements were repeated after 10 days. Results: There was no statistically significant difference between both software programs regarding the volume and MCA measurements with mean difference of 0.13 cm3 and 11.31 cm2 respectively (P ≤ 0.05). It was noticed that InVivo 5 yielded insignificantly higher mean values of the PAS volume and MCA. There was perfect inter and intra-observer agreement with ICC > 0.9. Conclusions: Both software programs; InVivo 5 Anatomage and Planmeca Romexis can be utilized for visualization and measurement of the upper airway spaces for orthodontic diagnostic purposes interchangeably.