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An epidemiologic field study was conducted in the village of Borbòn in Esmeraldas province in northern Ecuador to compare different parasitologic methods in the diagnosis of infection with the Entamoeba histolytica/Entamoeba dispar complex. The results of two stool antigen detection assays (the Prospect Entamoeba histolytica microplate assay and the E. histolytica II assay) were compared with isoenzyme characterization of the amebic isolates. Nearly all (176 of 178, 98.9%) subjects were positive for intestinal parasites on direct microscopic examination, and cysts and/or vegetative forms morphologically consistent with the E. histolytica/E. dispar complex were recorded in 48 of 178 cases (27%). Culture in Robinson's medium was positive for amebic stocks in 89 (50%) of the 178 samples tested. Of the 37 isolates successfully stabilized, cloned, and characterized by zymodeme analysis, seven (18.9%) showed isoenzyme patterns of E. histolytica, whereas 26 (70.3%) showed patterns of E. dispar. The remaining four strains were identified as Entamoeba coli (three isolates; 8.1%) and Dientamoeba fragilis (one strain; 2.7%).The immunochromatographic tests showed different degrees of sensitivity and specificity when compared with isoenzyme characterization as the reference technique. The microplate assay, which does not discriminate between E. histolytica and E.dispar, showed a sensitivity of 54.5% and a specificity of 94% for both these amebic species. In contrast, the second-generation E. histolytica II test had a sensitivity of 14.3% and a specificity of 98.4% for E. histolytica sensu stricto. Our survey clearly demonstrated that more specific and sensitive diagnostic tests, such as stool antigen detection assays and isoenzyme analysis, are needed to establish the actual worldwide distribution of E. histolytica and E. dispar.