Fecal samples collected from 245 cats over a 6-month period were analyzed for the presence of Clostridium difficile. After culture on selective media, isolates were identified by a latex agglutination test, and the presence of toxin A and toxin B gene sequences was determined by polymerase chain reaction. Clostridium difficile was isolated from 23 (9.4%) of the cats, and 34.8% of that group were colonized with toxigenic strains. All of the cats colonized with toxigenic C. difficile had > or = 1 of the risk factors (antibiotic use, antineoplastic therapy, immunosuppressive virus infection) associated with C. difficile infection in humans. Clostridium difficile was not found in any of the cats from a clinically healthy outpatient group of cats examined from the same hospital nor in cats from a specific-pathogen-free research colony on the same campus tested during the same time period. The data obtained in this study confirm the presence of C. difficile in cats at a veterinary teaching hospital. DNA fingerprinting analysis of these isolates allowed separation of the strains into 5 groups. Type 4 strain found in 7 cats was also recovered from the floor drain in the same hospital, suggesting a possible source of infection. Whether the organism is of clinical significance in diarrheal diseases of cats remains to be determined.