Confinement of horses with their heads elevated for periods up to 24 hours was used to evaluate the extent and the effects of bacterial contamination of the equine lower respiratory tract. Significant (P < 0.05) increases in bacterial numbers (up to 10(9) colony forming units/mL in transtracheal aspirate derived samples) occurred within 6 or 12 hours in most horses. Pasteurella/Actinobacillus spp and Streptococcus spp were most commonly isolated. Lowering of the head for 30 minutes every 6 hours to facilitate postural drainage did not prevent multiplication of organisms to levels equivalent to those achieved by horses where the head was elevated for 24 hours. When horses were released from confinement and heads were no longer maintained in an elevated position, clearance of accumulated secretions and bacteria occurred within 8 to 12 hours. Thus, confinement with the head elevated resulted in significant bacterial contamination and multiplication within the lower respiratory tract during a period often encountered in routine management procedures, such as transportation. The clearance of accumulated secretions occurred over a prolonged period after release from such confinement.