The aim of this investigation was to do a comparative study on the deposition and clearance of inhaled bacteria between the lungs and tracheae of mice exposed to aerosols of bacteria. Two hundred and eighty-eight mice were divided into four groups (n = 72) and exposed to aerosols of Pasteurella haemolytica or Staphylococcus aureus in four replicates. The numbers of bacteria were determined in the trachea and lungs of mice sacrificed 0, 2, 4, 8, 12, 24, 48 and 72 hours postexposure. Results indicated that bacterial deposition was greater in lungs than in tracheae. No significant (p greater than 0.05) difference was observed between P. haemolytica and S. aureus clearance rates. Although bacteria were rapidly eliminated from the whole respiratory tract, bacterial clearance was significantly (p less than 0.002) faster in tracheae than lungs. A significant (p less than 0.05) replicate effect was also observed.