To evaluate lesions of ammonia exposure and Mycoplasma pulmonis infection in gnotobiotic F344/N rats, groups of rats were inoculated with M. pulmonis, exposed to 76 micrograms/liter (100 parts per million) ammonia, or both, or served as controls. Six rats from each group were killed 3, 5, 7, and 9 days after inoculation and their respiratory organs prepared for histologic examination. Lesions were assessed by subjective scoring and computerized morphometry, and results obtained by the two methods were compared to assess agreement of results. Lesions were limited to the nasal passages. Ammonia exposure resulted in hyperplastic and degenerative changes in the anterior nasal epithelium. Lesions of mycoplasmosis were more severe in ammonia-exposed than unexposed rats, but qualitative differences in lesions were not apparent. Results of the two methods agreed in assessment of submucosal inflammatory cell accumulation. Epithelial lesions were difficult to evaluate by both methods in infected, ammonia-exposed rats. In evaluation of lesions of ammonia exposure alone, agreement was adequate. Both methods indicated that exudates were significantly greater in ammonia-exposed infected rats than in non-exposed infected rats. Thus, scoring and morphometry provided similar assessments of differences in lesion severity among the treatment groups.