The black-footed ferret (Mustela nigripes) is an endangered mustelid native to North America. Gastroenteritis is a documented cause of morbidity and mortality in managed individuals, particularly by infectious agents. Fecal cytology is an inexpensive and rapid test that can help guide clinical management strategies for animals with enteritis; however, normal parameters have not been established in black-footed ferrets. The objective of this study was to characterize fecal cytological findings of 50 fecal samples from 18 black-footed ferrets that received two different diet types (ground meat versus whole prey) and that were visibly judged to be normal or abnormal. This study also tested for the presence of Clostridium perfringens enterotoxin by enzyme-linked immunosorbent assay in all abnormal and a subset of normal fecal samples. Significantly higher spore-forming bacteria and yeast prevalence were present in normal feces from individuals following the meat-based compared with the whole-prey diet. Samples from individuals with abnormal feces had significantly more spore-forming bacteria than normal feces, regardless of diet. Normal feces had higher diplococci and spore-forming bacteria compared with domestic canine and feline standards. A single abnormal fecal sample was positive for enterotoxin and originated from the only animal requiring treatment. Results indicate that low numbers of spore-forming bacteria can be found in fecal samples from clinically normal black-footed ferrets. Fecal cytology shows significantly increased spore-formers in clinically abnormal ferrets and in clinically normal ferrets following a ground meat–based diet.