Purpose <p>To investigate the anatomical variations and measure the distances between surgically relevant structures in the maxilla associated with Le Fort I osteotomy in patients with maxillary canting using cone beam computed tomography (CBCT).</p> Methods <p>CBCT scans of 63 patients (21 males and 42 females) with maxillary canting who were indicated for orthognathic surgical planning were retrospectively investigated and analyzed. The distances of the relevant anatomical structures, including the descending palatine artery, pterygomaxillary junction, infraorbital foramen, and nasolacrimal duct opening, were measured with the key anatomical landmarks to evaluate their variations. The independent correlations of measurements with magnitude of canting were examined, considering a 5% significance level.</p> Results <p>Among the 63 patients, the mean vertical difference of maxillary canting was 3.26 ± 0.98&#xa0;mm and 3.62° ± 1.09°. The descending palatine artery differed significantly in distance between the longer and shorter sides (<i>P</i> &lt; 0.001). Similar significant differences were found in the pterygomaxillary junction distance (<i>P</i> &lt; 0.001), pterygomaxillary junction height (<i>P</i> &lt; 0.001), and infraorbital foramen distance (<i>P</i> = 0.009). Every 1&#xa0;mm of maxillary canting increases the pterygomaxillary junction distance by 0.1721&#xa0;mm, pterygomaxillary junction height by 0.2773&#xa0;mm, infraorbital foramen by 0.3301&#xa0;mm, and nasolacrimal duct in 0.2255&#xa0;mm.</p> Conclusion <p>Maxillary canting significantly affects the morphometrics of pterygomaxillary junction distance and height, infraorbital foramen, and nasolacrimal duct on the longer and shorter sides. Therefore, these surgical anatomies should be of concern when performing Le Fort I osteotomy in patients with maxillary canting.</p> Clinical trial number <p>Not applicable.</p>