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To investigate short- and long-term three-dimensional changes of pharyngeal airway morphology and hyoid bone position in dento-skeletal class III deformity patients after 2-jaw orthognathic surgery with segmentation.A retrospective analysis has been performed on patients with dento-skeletal class III deformity who had undergone orthognathic 2-jaw surgery with segmentations, presenting both pre- and post-surgical cone-beam computed tomographys. Three-dimensional skeletal movements, pharyngeal airway changes and hyoid bone position were measured and correlated.The mean short term postsurgical review period for all included 47 patients was 5.8 ± 2.2 months. Thirteen patients among them provided a mean long term period of 26.4 ± 3.4 months. The mean postsurgical maxillary movement was 2.29 ± 2.49 mm in vertical, 2.02 ± 3.45 mm in horizontal direction, respectively, while the mandibular movement was 6.49 ± 4.58 mm in vertical, and −5.85 ± 6.13 mm in horizontal direction. In short-term, the vertical length of nasopharynx was found to be reduced (P = 0.005) but increased for the oropharynx (P < 0.001). Furthermore, the oropharyngeal minimum cross-sectional area has decreased significantly (P = 0.013). The hyoid bone moved posterosuperiorly, however, with only its horizontal movement found to be significant (P = 0.043). No significant result was detected in long-term analyses, neither in postsurgical pharyngeal airway changes nor the hyoid bone movement. There were no significant differences in pharyngeal airway measurements (P > 0.05) detected between patients with and without genioplasty advancement.Two-jaw orthognathic surgery in dento-skeletal class III patients led to a statistically non-significant reduction of the post-surgical airway volume in both short- and long-term. Although the post-surgical oropharyneal minimum cross-sectional area was decreased significantly in the short term, this finding did not persist in the long term.