Background. HIV is prevalent throughout South Africa, and diarrhoea is a common presentation to the emergency department (ED) among both HIV-infected and -uninfected individuals.  Method. We audited the management of diarrhoea against standard guidelines in the ED of a regional hospital in KwaZulu-Natal. Patients presenting with diarrhoea as their chief complaint were eligible and data were collected prospectively.  Results. A total of 72 patients were included: 58 (81%) of patients were HIV-positive with an average CD4+ count of 180 cells/µl. A total of 34 stool samples were sent for standard microscopy and culture (M&C), among which 26 were positive (76%). Forty-three patients (60%) received antibiotics, 15 of whom had positive stool M&C. In all cases, the final diagnosis was listed as acute gastroenteritis without further specification, and antibiotic use according to guidelines appeared inconsistent.  Conclusion. Based on this audit, we suggest that current guidelines are not clear concerning management of acute diarrhoea in HIV-infected individuals, and that the lack of clear management strategies is likely to affect patient safety and increase antibiotic resistance.