Amoebiasis is a common and life-threatening disease. The discrimination of the pathogenic Entamoeba histolytica from the non-pathogenic Entamoeba dispar could be done by advanced methods such as enzyme immunoassay (EIA) and PCR. The aim of this study was to investigate the prevalence of amoebiasis in Izmir province, and differentiate the Entamoeba species by PCR and EIA. Stool samples of 2,047 individuals were examined by direct microscopy, formalin ethyl acetate concentration, trichrome staining and culture, and those found to be positive for E. histolytica/dispar by any of these methods were further analyzed by PCR and EIA for species identification. Fifty-nine of 2,647 (2.9%) stool samples were found to be positive for E. histolytica/dispar with microscopy and/or culture. Among these positive samples, E. histolytica was detected in 14 (23.7%) and 5 (8.5%) samples with PCR and antigen-specific ELISA (EIA), respectively. E. dispar was diagnosed in 31 (52.5%) and 52 (88.1%) of 59 samples with species-specific PCR and EIA, respectively. Risk factors related to infection with Entamoeba spp. and other intestinal parasites included living in shanty houses (p<0.01), a history of recent immigration to Izmir (p<0.01), having no social security (p<0.05) and living with a crowded family (p<0.01). The results demonstrated the significance of amoebiasis as a public health problem among people with low socio-economic status in Izmir province.