The purpose of this study was to investigate morphologic changes in oropharyngeal structures in mandibular prognathic patients after orthognathic surgery. The study consisted of 25 patients (12 males and 13 females) with mandibular prognathism who underwent surgical and orthodontic treatment. A set of 4 standardized lateral cephalograms were obtained from each subject preoperatively and at 3 months, 6 months, and 1 year postoperatively. Morphologic changes in upper airway structures were evaluated longitudinally by gender. Parameters of the anteroposterior width of the pharynx significantly decreased at 3 and 6 months in both genders, and these parameters tended to rebound to the preoperative values 1 year postoperatively in females, but not in males. The hyoid bone significantly descended inferiorly 1 year postoperatively in males, while there were no significant changes in females. The distance between the hyoid bone and the third vertebra gradually decreased in males postoperatively; however, there were no significant changes in females. The cross-sectional area of the hypopharynx significantly decreased 1 year postoperatively in males, but not in females. These results indicate that the upper airway morphology changed differently in males and females following surgery. To compensate for skeletal changes following surgery, it appears that males and females responded in different ways to preserve a functional upper airway.