For a variety of head and neck cancers, specifically those of the oropharynx, larynx, and hypopharynx, minimally invasive trans-oral approaches have been developed to reduce perioperative and long-term morbidity. However, in trans-oral surgical approaches anatomical deformation due to instrumentation, specifically placement of laryngoscopes and retractors, present a significant challenge for surgeons relying on preoperative imaging to resect tumors to negative margins. Quantifying the deformation due to instrumentation is needed in order to develop predictive models of operative deformation. In order to study this deformation, we used a CT/MR-compatible laryngoscopy system in concert with intraoperative CT imaging. 3D models of preoperative and intraoperative anatomy were generated. Mandible and hyoid displacements as well as tongue deformations were quantified for eight patients undergoing diagnostic laryngoscopy. Across patients, we found on average 1.3 cm of displacement for these anatomic structures due to laryngoscope insertion. On average, the maximum displacement for certain tongue regions exceeded 4 cm. The anatomical deformations quantified here can serve as a reference for describing how the upper aerodigestive tract anatomy changes during instrumentation and may be helpful in developing predictive models of intraoperative upper aerodigestive tract deformation.