High prevalences of intestinal amoebiasis are commonly reported by microscopy in Ethiopia. In order to confirm the actual occurrence of Entamoeba histolytica we collected 108 stool specimens from different hospitals & health centers from patients in whom haematophagous trophozoites were believed to be found. We detected only a single E. histolytica case while 77 (71.3%) were E. dispar and the remaining 30 samples were negative for both species by real-time PCR based on the small subunit ribosomal RNA gene sequence of E. histolytica and E. dispar. The tradition of microscopy in a routine diagnostic set-up appears unsatisfactory to reliably differentiate rbc-engulfing amoeba from non-invasive amoeba in wet smears.