Two types of commonly used contact bedding, aspen chip and corncob, were analyzed for the presence of fungal spores after two rats in a toxicology study were diagnosed with fungal rhinitis. A range of 700 to 5440 spores per g consisting of six species of fungus (Cladosporidium, Acremonium, Penicillium, Aspergillus, Fusarium, and Scolobasidium) were isolated from non-autoclaved corncob bedding obtained from two vendors. Negligible spore counts were detected in autoclaved corncob bedding and from either autoclaved or non-autoclaved aspen chip bedding. The present study demonstrates that high fungal spore counts may occur in untreated corncob bedding and that these may be associated with opportunistic disease in healthy, non-immunosuppressed animals. Autoclaving reduced the viable fungal spore load to an undetectable level.