We determined the prevalence of Entamoeba (E.) histolytica, E. dispar and E. moshkovskii in Patients with chronic diarrhoea associated with abdominal pain or discomfort mimicking irritable bowel syndrome. Stool samples were collected from 161 Patients with chronic diarrhoea and from 157 healthy controls. Stool microscopy with modified trichrome stain, culture and polymerase chain reaction (PCR) for Entamoeba spp. differentiation was performed. Microscopy demonstrated Entamoeba cysts in 44% (57/129) of Patients with diarrhoea compared to 29% (44/151) of controls (P = 0.009). In Patients with diarrhoea, PCR for E. histolytica was positive in 9% (11/129) (P = 0.008), E. dispar in 19% (24/129) (P = 0.117) and E. moshkovskii in 19% (24/129) (P < 0.001). E. histolytica and E. moshkovskii were significantly associated with diarrhoea while E. dispar was found equally in both groups.