Isolates of the cilia-associated respiratory (CAR) bacillus were harvested from the trachea of three naturally infected rats and five naturally infected rabbits and were grown on 3T3 mouse fibroblast cells. Isolates were compared by growth characteristics in mammalian cell culture, by use of protein and DNA analyses, and by experimental infections of BALB/c mice. Examination of CAR bacillus isolates by transmission electron microscopy indicated that organisms from rats and rabbits were similar in appearance and had an acidic mucopolysaccharide layer. In culture, the isolates from rats appeared larger than the rabbit isolates and formed large multiorganism aggregates, whereas isolates obtained from rabbits did not. Protein and antigenic analyses and DNA ribotyping revealed minor differences between isolates but could not be used to distinguish the rat from the rabbit isolates. Mice experimentally inoculated with CAR bacillus of rat origin developed interciliary colonization, seroconverted, and developed microscopic pulmonary lesions. Mice inoculated with isolates of rabbit origin did not display intraciliary colonization, seroconvert, or develop pulmonary disease. The findings of this study indicate that CAR bacillus isolates of rat and rabbit origins may be distinct strains and suggest that, in mice, isolates of rat origin may be more virulent than those of rabbit origin.