The aim of the study was to identify craniofacial and pharyngeal anatomical factors directly related to obstructive sleep apnoea (OSA). The design and setting was a hospital-based, case-controlled study. Ninety-nine subjects (78 males and 21 females) with a confirmed diagnosis of OSA, who were referred to the Dental Hospital for construction of a mandibular advancement splint were recruited. A similar number of control subjects, matched for age and sex, were recruited after completing snoring and Epworth Sleepiness Scale questionnaires to exclude habitual snoring and daytime sleepiness. An upright cephalogram was obtained and skeletal and soft tissue landmarks were traced and digitized. In OSA subjects the anteroposterior skeletal measurements, including maxillary and mandibular length were reduced (P < 0.001). The intermaxillary space was found to be 3.1 mm shorter in OSA subjects (P = 0.001). The nasopharyngeal airway in OSA subjects was narrower (P < 0.001) but pharyngeal length showed no difference. The tongue size was increased (P = 0.021), soft plate length, thickness and area were all greater (P < 0.001) and the hyoid bone was more inferiorly positioned in OSA subjects (P < 0.001). This study identifies a significant number of craniofacial and pharyngeal anatomical factors directly related to OSA.