ABSTRACT Background and objective Craniofacial structure is an important determinant of obstructive sleep apnoea (OSA) syndrome risk. Three‐dimensional stereo‐photogrammetry (3dMD) is a novel technique which allows quantification of the craniofacial profile. This study compares the facial images of OSA patients captured by 3dMD to three‐dimensional computed tomography (3‐D CT) and two‐dimensional (2‐D) digital photogrammetry. Measurements were correlated with indices of OSA severity. Methods Thirty‐eight patients diagnosed with OSA were included, and digital photogrammetry, 3dMD and 3‐D CT were performed. Distances, areas, angles and volumes from the images captured by three methods were analysed. Results Almost all measurements captured by 3dMD showed strong agreement with 3‐D CT measurements. Results from 2‐D digital photogrammetry showed poor agreement with 3‐D CT. Mandibular width, neck perimeter size and maxillary volume measurements correlated well with the severity of OSA using all three imaging methods. Mandibular length, facial width, binocular width, neck width, cranial base triangle area, cranial base area 1 and middle cranial fossa volume correlated well with OSA severity using 3dMD and 3‐D CT, but not with 2‐D digital photogrammetry. Conclusion 3dMD provided accurate craniofacial measurements of OSA patients, which were highly concordant with those obtained by CT, while avoiding the radiation associated with CT. Craniofacial structure is an important determinant of obstructive sleep apnoea (OSA) syndrome risk. Rapid quantitative analysis of facial surface morphology is needed for large population‐based studies. Radiation‐free three‐dimensional stereo‐photogrammetry provides accurate craniofacial measurements in patients with OSA which are highly concordant with those obtained by computed tomography. See related Editorial