We evaluated the usefulness of a multiplex-PCR method for differentiation of Entamoeba histolytica and Entamoeba dispar, which are morphologically indistinguishable species. Cultured trophozoites of E. histolytica HM-1: IMSS and E. dispar SAW were used as the positive control. Seven human fecal samples, from which E. histolytica-like cysts were detected by microscopic examination, and three intestinal protozoan parasites, Cryptosporidium parvum HNJ-1, Giardia intestinalis Portland-1, and Blastocytis hominis Nand II, were used for the evaluation of sensitivity and specificity of the PCR method. The other PCR method, which has been used for the diagnosis of amebic infections in Japan, was also performed by using the same samples for the evaluation. In comparison with the conventional PCR method, the multiplex-PCR showed 1) higher sensitivity, 2) the size of diagnostic fragments of PCR products was clearly different in both Entamoeba species, 3) it was possible to perform PCR using a single tube per sample, and then to save the amount of DNA polymerase, 4) no diagnostic amplification products were found in other intestinal protozoan parasites, and 5) E. histolytica specific fragment was amplified in all clinical samples examined. In conclusion, it is considered that the multiplex-PCR method is a useful tool for detection of both Entamoeba species DNA from fecal samples and for the distinction between E. histolytica and E. dispar.