Tracheal mucociliary clearance was determined in horses by measuring the rostrad transport of the radiopharmaceutical 99mtechnetium-sulphur colloid following deposition on the tracheal epithelium by intratracheal injection. The effects of head position (head elevated to normal standing position vs head lowered) and of accumulated purulent secretions on tracheal mucociliary clearance were evaluated for the first time in the horse. In normal horses tracheal mucociliary clearance was greatly accelerated by lowering the head so that the cranial trachea was lower than the caudal trachea. Horses confined with their heads elevated for 24 hours developed an accumulation of purulent airway secretions (and associated increased numbers of bacteria) in the lower respiratory tract and showed a decrease in tracheal mucociliary clearance when compared with their previously measured rate when the lower airway contained only normal secretions. These findings have implications for management practices where horses are prevented from lowering their heads, such as transportation and cross-tying, which may therefore contribute to lower respiratory tract disease in horses.