Chronic diarrhea is not uncommon in horses and can be a real difficult problem to diagnose and treat.  Most of the horses are healthy otherwise but seem to have continual or intermittent diarrhea that does not respond to changes in feed or deworming medications.  Dr. Ashley Whitehead from the University of Calgary indicates at the AAEP convention that basic diagnostic bloodwork is required as well as fecal egg counts to check for parasites.  There is also an equine diarrhea panel that can identify disease-producing organisms in the horse’s intestine.  However, some of these organisms are normally found in the horse’s intestine so this test may not be helpful unless the bacteria Salmonella is found. 

Unfortunately, 30% of the cases remain undiagnosed as it is difficult to determine the cause in many cases.  Other causes include sand accumulation in the intestine, which your vet can test for.  Also, inflammatory bowel disease and intestinal lymphoma can cause intermittent diarrhea but can only be diagnosed by an intestinal biopsy, which is not an easy process in a horse.  A sample can be taken from the rectum and analyzed and that can aid in the diagnosis if the condition is in the rectum.  Malabsorption can lead to diarrhea in horses and there are tests for glucose that can be used to diagnose that.  And some horses have a condition called intestinal dysbiosis in which the bacteria in the intestine is abnormal and giving a horse intestinal contents from a healthy horse through a nasogastric tube may be helpful.  Although pre- and probiotics are commonly used in these cases, this treatment is not effective in many horses.  Sometimes trial and error with different feeds and different medications are required to treat these chronic diarrhea cases.