Pneumonia is a common complication of boid inclusion body disease (BIBD) in snakes. The tracheal mucociliary apparatus of eight boas (Boa constrictor) and two pythons (Python regius, Morelia viridis) was examined to assess whether absent or reduced mucociliary clearance could be a predisposing factor. Nine of the examined snakes were positive for BIBD by detection of inclusion bodies and three had lung pathologies other than the formation of inclusion bodies. A considerable individual variation of ciliary beat frequency (CBF, 3.0 ± 0.75 Hz to 7.8 ± 1.27 Hz), transport speed (23.1 ± 12.56 μm/sec to 189.2 ± 41.17 μm/sec), and transport direction (−12.5° ± 11.43° to 36.1° ± 7.53°) was found. CBFs of the BIBD-affected snakes with or without lung pathologies were markedly lower than ranges published for birds or mammals, but the net transport speeds and directions lay well within. The present investigation does therefore not reveal any signs of an inadequate mucociliary clearance in BIBD-affected snakes.