Although Clostridium difficile is recognized as a cause of enterocolitis in horses and humans, there has been little work published regarding the lability of C. difficile and its toxins in feces. A significant decrease in recovery of C. difficile from inoculated equine fecal samples occurred during storage. Recovery after storage in air at 4 degrees C decreased from 76% (37/49) after 24 hours to 67% (33/49) at 48 hours and 29% (14/ 49) after 72 hours. In contrast to aerobic storage, 25 of 26 samples stored anaerobically at 4 degrees C yielded growth of C. difficile for 30 days, whereas the organism was only detected for 2.5 +/- 2.52 days (x +/- SD) in paired samples stored aerobically. The use of an anaerobic transport medium was effective in maintaining viability of C. difficile. These findings indicate that poor aerotolerance is the reason for the rapid decrease in culture yield. In contrast to C. difficile organisms stored aerobically at 4 degrees C, C. difficile toxins were considerably more stable and could be detected by enzyme-linked immunosorbent assay in both broth and inoculated fecal samples for at least 30 days. The poor survival of C. difficile but the stability of its toxins when feces are stored aerobically must be considered when submitting samples for diagnosis of C. difficile-associated enterocolitis in horses and when interpreting laboratory results.