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Vomiting and diarrhoea in dogs and cats are two of the most common maladies facing the small animal practitioner today, and bacterial, viral and parasitic enteropathogens play an important role in many of these cases. Dogs and cats harbouring intestinal parasites or even bacterial pathogens can remain asymptomatic, but may develop clinical signs ranging in severity from a mild, selflimiting diarrhoea, to a potentially fatal acute haemorrhagic diarrhoeal syndrome. Evaluation of the animal's history and physical examination are integral to formulating an appropriate list of differential diagnoses ranking the most likely infectious agents involved. This chapter explains Faecal examination; Intestinal parasites; Enteropathogenic bacteria; Viral infections; and Intestinal fungal infections.