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Background In equine athletes, dynamic stenotic disorders of the upper airways are often the cause for abnormal respiratory noises and/or poor performance. There are hypotheses, that head and neck flexion may influence the morphology and function of the upper airway and thus could even induce or deteriorate disorders of the upper respiratory tract. Especially the pharynx, without osseous or cartilaginous support is prone to changes in pressure and airflow during exercise. The objective of this study was to develop a method for measuring the pharyngeal diameter in horses during exercise, in order to analyse whether a change of head-neck position may have an impact on the pharyngeal diameter. Results Under the assumption that the width of the epiglottis remains constant in healthy horses, the newly developed method for calculating the pharyngeal diameter in horses during exercise is unsusceptible against changes of the viewing-angle and distance between the endoscope and the structures, which are to be assessed. The quotient of the width of the epiglottis and the perpendicular from a fixed point on the dorsal pharynx to the epiglottis could be used to determine the pharyngeal diameter. The percentage change of this quotient (pharynxepiglottis- ratio; PE-ratio) in the unrestrained head-neck position against the reference position was significantly larger than that of any other combination of the head-neck positions investigated. A relation between the percentage change in PE-ratio and the degree of head and neck flexion could not be confirmed. Conclusions It could be shown, that the pharyngeal diameter is reduced through the contact position implemented by the rider in comparison to the unrestrained head and neck position. An alteration of the pharyngeal diameter depending on the degree of head and neck flexion (represented by ground and withers angle) could not be confirmed. [ABSTRACT FROM AUTHOR]