Purpose <p>The main purpose of this study is to evaluate the facial morphology of obstructive sleep apnoea (OSA) individuals by using a handheld blue light three-dimensional (3D) scanner (HBL-3DS) in comparison to conventional lateral cephalometric radiography (LCR). Moreover, our research question is to explores the correlation between 3D facial and neck measurements with OSA indices, encompassing the hypoxic burden.</p> Method <p>This prospective cross-sectional study included forty-four adults with OSA. We compared three measurements between LCR and HBL-3DS images: modified facial profile angle (MFPA), nasolabial angle (NLA), and mandibular length (ML). Additionally, the 3D images of thirty-four participants with OSA indices were analysed for seventeen parameters, such as angles, ratios, and linear distances.</p> Results <p>This study revealed significant strong correlations (<i>p</i> &lt; 0.001) between LCR and HBL-3DS in the measurements of MFPA (<i>r</i> = 0.675), NLA (<i>r</i> = 0.723), and ML (<i>r</i> = 0.675). However, no significant correlation was found between all predictors and the Apnoea-Hypopnea Index (AHI) or Oxygen Desaturation Index (ODI) in the 3D images of the thirty-four participants. Multivariate regression analysis demonstrated an independent negative correlation between mandibular width (MW) and nadir oxygen levels, while an independent positive correlation was observed between inner canthal width and the Rapid-Eye-Movement percentage (REM).</p> Conclusions <p>The study highlighted a significant association between LCR and HBL-3DS. HBL-3DS delivers precise 3D facial and neck measurements, presenting itself as a potentially cost-effective, radiation-free, and portable screening method for participants with OSA in clinical settings.</p>