Background: The present study evaluated the three-dimensional changes of the pharyngeal airway after orthognathic surgery (OGS) between patients with unilateral and bilateral clefts and between patients with unilateral cleft with and without pharyngeal flap (PF).

Methods: This study enrolled nonsyndromic patients with unilateral (N = 27) or bilateral (N = 18) cleft lip/palate who received cleft OGS for midface retrusion and/or malocclusion between 2015 and 2020. Cone-beam computed tomography images were obtained before (T0) and after (T1) cleft OGS. We measured the velopharyngeal, oropharyngeal, and hypopharyngeal airway volumes, minimal cross-sectional area, and the horizontal displacement of anterior nasal spine, A point, B point, and pogonion.

Results: The patients with bilateral cleft exhibited smaller initial velopharyngeal airway volume (unilateral: 8623 mm3; bilateral: 7781 mm3; p = 0.211). A significant increase in the velopharyngeal airway volume (median volume = 744 mm3) was observed among patients with bilateral cleft (p = 0.031). The median horizontal displacement of A point was 2.9 and 2.6 mm among the patients with unilateral and bilateral clefts, respectively (p = 0.276), and the median horizontal displacement of B point was −2.9 and −3.3 mm among patients with unilateral and bilateral clefts, respectively (p = 0.618). The patients with unilateral cleft with PF exhibited lower initial velopharyngeal airway volume (PF+: 7582 mm3; PF–: 8756 mm3; p = 0.129) and a lower increase in velopharyngeal airway volume (PF+: 437 mm3; PF–: 627 mm3; p = 0.739) after OGS.

Conclusions: Midface hypoplasia and the decrease in the velopharyngeal airway volume were more significant among the patients with bilateral cleft and the patients with unilateral cleft with PF. After OGS, the velopharyngeal airway volume considerably increased among the patients with bilateral cleft, but no considerable differences were noted among the patients with unilateral cleft with PF.