In an effort to improve the diagnosis of intestinal amoebiasis, a real-time PCR has been used for the detection and differentiation of Entamoeba histolytica and E. dispar infections in African or South American immigrants who live in Spain. Faecal samples from all of the 130 subjects had apparently been found to contain E. histolytica/E. dispar cysts by microscopical examination. Using the real-time PCR, E. histolytica DNA was detected in faecal samples from only 10 (7.7%) of the immigrants, with E. dispar DNA detected in the samples from another 117 (90.0%) of the subjects. The use of such PCR in the routine investigation of patients found positive for E. histolytica/E. dispar cysts (by microscopy) is recommended, especially in non-endemic areas.