The purpose of this study was to compare two groups of adult men from different ethnic backgrounds and with obstructive sleep apnea; they were selected by matching age, gender, skeletal pattern, body mass index, and respiratory disturbance index. Pretreatment cephalometric radiographs and overnight polysomnograms of 30 Chinese and 43 Caucasian patients with Class II, Division 1 malocclusions were analyzed to investigate if there were craniofacial and upper airway structural differences between the two ethnic groups. The Chinese group, when compared with the group of Caucasian patients, revealed more severe underlying craniofacial skeletal discrepancies with significantly smaller maxilla and mandibles, more severe mandibular retrognathism, proclined lower incisors, increased total and upper facial heights, and steeper and shorter anterior cranial bases. However, no significant differences were found between the two groups in posterior facial height, ratio of upper to lower anterior facial height, and the position of hyoid bone, maxilla, and upper incisors. With regard to soft tissue and upper airway measurements, there were no significant ethnic differences in tongue and soft palate size, vertical length of oropharynx, and anteroposterior dimensions of the upper airway at most of the levels except for a larger super-posterior airway space, a larger nasopharynx and oropharynx cross-sectional area, and a smaller tongue height in the Chinese group. We conclude that there are a number of craniofacial and upper airway structures that differ between the two ethnic groups that may be relevant to the treatment of obstructive sleep apnea in various ethnic groups.