Streptococcus pneumoniae was isolated from specific-pathogen-free rodents in two rooms at a commercial breeding facility during vendor surveillance testing. In a survey of 274 animals from the two rooms over a period of 7 months, capsular serotype 35 S. pneumoniae was isolated from the upper respiratory tracts of 11% (9 of 82) of C57BL/6 mice in room A and 14% (10 of 72) of F344 rats in room B, but not from WKY rats, BALB/c mice or DBA/2 mice from room A. In both C57BL/6 mice and F344 rats, older rodents had higher colonization frequencies. Nasal lavage cultures gave the best results in identifying colonized rodents. No clinical illness or microscopic lesions were associated with pneumococcal colonization in rats or mice, and no other evidence of potential pathogen infection was found except for positive serologic tests for mouse rotavirus in mice. This is the first report of natural pneumococcal infection in mice, and the first report of type 35 S. pneumoniae infection in rodents. The findings support an earlier observation that pneumococcal infections in rat colonies tend to be monotypic and suggest that the same may be true in mice.