Cilia-associated respiratory (CAR) bacillus was detected by means of the reverse transcription (RT)-polymerase chain reaction (PCR), and the results were compared with those of indirect immunofluorescence test (IFAT) for the detection of the organism. In the experimental infections, 15 mice were in contact with mice previously inoculated with CAR bacillus. Three mice each were tested at days 3, 5, 7, 12 and 20 postexposure. On day 3 postexposure, CAR bacillus was detected in oral swab samples from all 3 mice by RT-PCR, but was not detected in any sampling sites from the mice by IFAT. Total numbers of positive samples from nasal, oral and tracheal swabs obtained through the test were 6/15, 14/15 and 8/15, respectively, by RT-PCR, and 2/15, 6/15 and 3/15, respectively by IFAT. For the detection of CAR bacillus in samples from 52 rats, 34 serum antibody negative rats by enzyme-linked immunosorbent assay were also negative by RT-PCR and IFAT except for one sample from the oral cavity, and all serum antibody positive rats were positive for the organism by RT-PCR but it could not be detected in five of them by IFAT. By means of RT-PCR, no differences in the positive rates depending on sampling sites were observed except in one rat. The RT-PCR was found to be a specific, highly sensitive and reliable procedure for detecting CAR bacillus in mice and rats. The oral cavity was the most suitable site for the diagnosis of the early stage of this infection by RT-PCR.