Objectives: Our purpose was to compare the ciliary function between the upper and lower airway. Methods: Basal ciliary beat frequency (CBF) and changes in CBF in response to exogenous stimuli [adenosine triphosphate (ATP) or benzalkoniunn chloride (BAC)] of primary cultured mouse nasal and tracheal epithelial cells were quantified using digital microscopy combined with a beat-by-beat CBF analysis. Results: The basal CBF of the mouse tracheal culture was statistically higher than the nasal culture. Adding 10 or 100 p,m ATP caused an increase of CBF in both mouse nasal and tracheal cultures; however, nasal culture induced a more robust increase of CBF than tracheal culture. Treatment with 0.001% BAC increased CBF within 2 min after treatment and then CBF gradually decreased; nasal and tracheal culture manifested a similar change in CBF. With a concentration of 0.01%, BAC induced a rapid and time-dependent decrease of CBF in both mouse nasal and tracheal cultures; however, tracheal culture showed a blunter response to this ciliotoxic agent, with the ciliary beating duration time distinguishably longer than in the nasal culture. Conclusion: The inherent ciliary and physiological function is different in the upper and lower airway in mice. Copyright (C) 2012 S. Karger AG, Basel