Diseases of the larynx and trachea are a heterogenous group of disorders. Their diagnosis frequently requires invasive methods. Ultrasound is a non-invasive, repeatable and safe diagnostic method, which has recently, thanks to the development of technology, provided for very accurate imaging of even small structures, as well as their assessment on dynamic examination. Ultrasound examination of the larynx and trachea will be performed in 2022–2023 in a group of randomly selected 300 stable neonates born between 32 and 42 weeks of gestation. The results of this study will be presented after data collection in accordance with the adopted methodology. To date, this will be the first study to describe the ultrasound anatomy of the larynx and trachea and to establish reference ranges for the size of individual structures of the larynx and trachea in the neonatal population. We expect that our study will contribute to the further development of this part of ultrasonography and will reduce the number of invasive procedures performed in the diagnostics of these organs in the future. This manuscript is a study protocol registered at ClinicalTrials.gov (Identifier NCT05636410) and approved by the Bioethics Committee of the Medical University of Warsaw (KB 65/A2022).