The cilia-associated respiratory (CAR) bacillus is an unclassified, gram-negative bacterium that has been implicated as an etiologic agent of respiratory tract disease in laboratory rodents. A morphologically and antigenically similar organism has been identified in rabbits and is thought to be a related bacterium, although clinical signs of disease and histologic lesions are absent in infected rabbits. To compare the pathogenicity of rat- and rabbit-origin CAR bacillus isolates in rabbits, neonatal rabbits were experimentally infected with CAR bacillus isolates obtained from an infected rat and rabbit. Rabbits experimentally inoculated with rabbit-origin CAR bacillus had a nasal discharge, seroconverted and developed histologic lesions, whereas rabbits inoculated with rat-origin CAR bacillus seroconverted but did not have evidence of colonization of the respiratory tract. The CAR bacillus isolates were further examined at the genetic level by sequencing 1,261 base pairs of the 16S rRNA gene from six CAR bacillus isolates obtained from infected rabbits. A consensus sequence was obtained and compared with the analogous gene sequence data from rat-origin CAR bacillus isolates. Results indicated that these two organisms are distinctly different, with only 48.8% sequence homology. Comparison of the rabbit-origin 16S rRNA gene sequence with the database Genbank indicated that the organism is most closely related to members of the genus Helicobacter. Bacteria with the highest percentage of similarity with the rabbit-origin CAR bacillus were Helicobacter sp. strain Seymour and H. felis, with 91.1 and 90.8%, respectively. Findings of this study indicate that CAR bacillus isolates from rats and rabbits are host-specific and are different bacteria that belong to distinct genera.