Dynamic nasopharyngeal collapse with upper airway obstruction is an important cause of exercise intolerance in performance horses. Its underlying pathophysiology is not fully understood. We hypothesize that head position affects pharyngeal diameter, and thus head position may be a contributing factor to nasopharyngeal obstruction. Fifteen adult healthy horses were subjected to endoscopy and radiography at rest. The pharyngeal diameter was measured at nine different head and neck positions. The effect of sedation and breathing cycle on the pharyngeal diameter was determined, and the relationship between the head angle and the pharyngeal diameter was analyzed. There was a significant influence of head and neck position on pharyngeal diameter, with head position having the major effect (P<0.001); neck position was less important, but still significant (P<0.05). The smallest pharyngeal diameter was found at the dorsal, flexed position, which is a clinically important head position in dressage horses. The largest pharyngeal diameter was found at the extended midway position. At each head level, the pharyngeal diameter decreased with flexing the head and it increased with extending the head. The head angle was not associated with pharyngeal diameter, and neither sedation status nor breathing cycle significantly affected pharyngeal diameter. A decrease in pharyngeal diameter will limit the airflow through the upper respiratory tract, and it may result in turbulence with subsequent dynamic collapse. Head and neck position should therefore be considered a possible contributing factor in horses with suspected nasopharyngeal dysfunction.