Aim: To investigate if the volumes of the naso and oropharynx have a relationship with sex, skeletal pattern, and breathing pattern. Materials and Methods: Cone beam computed tomography images of 298 individuals (144 men and 154 women) were classified according to skeletal malocclusion (Class I, II, or III), facial type (brachycephalic, mesocephalic, or dolichocephalic), and breathing pattern (nasal or oral breathing). The volumes of the nasopharynx, oropharynx, and total volume (combination of the volumes of the naso and oropharynx) of each individual was calculated through semiautomatic segmentation with ITK-SNAP software. The images were assessed by two dentomaxillofacial radiologists independently. Multi-way analysis of variance compared the data at a significance level of 5% (α=0.05). Results: Intra- and interevaluator agreement values ranged from 0.96 to 0.98, and from 0.77 to 0.94, respectively. The volume of the nasopharynx was related to sex, with men showing greater volumes than women (p=0.0197). For the oropharynx, brachycephalic individuals had greater volumes than dolichocephalics (p=0.0423); mesocephalic individuals showed intermediate volumes and did not differ from the other types (p>0.05). Skeletal malocclusion and breathing pattern did not have an association with the nasopharynx, oropharynx, and total volume (p>0.05). Conclusions: The volumes of the nasopharynx and oropharynx differ between individuals of different sexes and facial types, respectively. Conversely, there is no relationship between the volume of these regions and the skeletal malocclusions and breathing patterns.