The aetiology of obstructive sleep Apnoea (OSA) is multifactorial,consisting of a complex interaction between anatomic andneuromuscular factors and an underlying genetic predispositiontoward this common disorder. Although obesity is considered the majoranatomical risk factor for OSA, craniofacial morphology is increasinglyacknowledged as an important interacting factor. As such craniofacialmorphology is an important intermediate phenotype in the investigationof genetic susceptibility to OSA.Craniofacial morphology has been evaluated most extensively usingvarious imaging modalities including Cephalometric x-rays, CT and MRIscans. Each modality has unique strengths and limitations in their abilityto assess craniofacial anatomy. However, a key to large scale geneticstudies is the need for simple, cost-effective, high throughput methodsfor quantifying the craniofacial phenotype. Novel quantitative photogrammetrymethods have recently been reported, and hold promise asa phenotyping tool.Craniofacial characteristics associated with OSA include aspectsof skeletal morphology, as well as soft tissue morphology. Skeletalabnormalities include shorter maxilla and mandibular length,retroposition of the maxilla and mandible, maxillary constriction,inferior displacement of the hyoid bone, longer anterior face, steepmandibular plane, and overjet/overbite. Soft tissue abnormalitiesinclude enlargement of the tongue and soft palate, elongated uvula,adenotonsillar hypertrophy, enlargement of the lateral pharyngealwalls and parapharyngeal fat pads. It is the interaction between skeletaland soft tissues that determines the impact on upper airway size andfunction. The influences of growth, gender, and ethnicity on craniofacialmorphology are also gaining recognition.Craniofacial morphology is an important intermediate phenotype inthe pathway to OSA, and therefore is an essential element for the studyof OSA genetics. Novel high throughput photographic methods toquantify craniofacial and intraoral characteristics have the potential tofacilitate large scale genetic studies in OSA.