BACKGROUND: Giardia intestinalis, Cryptosporidium spp and Entamoeba histolytica are obligate pathogens and are the most common causative agents of childhood diarrhoea. The diagnosis of these parasitic infections was for a long time based on microscopic examination of stools that lacks sensitivity and specificity and requires a highly trained staff. As a result of these limitations, DNA-based detection methods exhibiting numerous advantages such as increased sensitivity and specificity, ability to combine multiple targets in one multiplex assay have been developed for enteric parasites. This study aimed to assess the epidemiology of these three-common diarrhoea-causing parasites in children under five years using microscopy vs. real time PCR assay.