The aim of this study was to describe the first development and evaluation of a multiplex tandem PCR (MT-PCR) assay for the detection and identification of 4 common pathogenic protozoan parasites, Cryptosporidium spp., Dientamoeba fragilis, Entamoeba histolytica, and Giardia intestinalis, from human clinical samples. A total of 472 fecal samples submitted to the Department of Microbiology at St. Vincent's Hospital were included in the study. The MT-PCR assay was compared to four real-time PCR (RT-PCR) assays and microscopy by a traditional modified iron hematoxylin stain. The MT-PCR detected 28 G. intestinalis, 26 D. fragilis, 11 E. histolytica, and 9 Cryptosporidium sp. isolates. Detection and identification of the fecal protozoa by MT-PCR demonstrated 100% correlation with the RT-PCR results, and compared to RT-PCR, MT-PCR exhibited 100% sensitivity and specificity, while traditional microscopy of stained fixed fecal smears exhibited sensitivities and specificities of 56% and 100% for Cryptosporidium spp., 38% and 99% for D. fragilis, 47% and 97% for E. histolytica, and 50% and 100% for G. intestinalis. No cross-reactivity was detected in 100 stool samples containing various other bacterial, viral, and protozoan species. The MT-PCR assay was able to provide rapid, sensitive, and specific simultaneous detection and identification of the four most important diarrhea-causing protozoan parasites that infect humans. This study also highlights the lack of sensitivity demonstrated by microscopy, and thus, molecular methods such as MT-PCR must be considered the diagnostic methods of choice for enteric protozoan parasites.Enteric protozoa continue to be the most commonly encountered parasitic diseases and to cause significant morbidity and mortality throughout both developed and developing regions of the world, affecting millions of people each year (22). While Blastocystis hominis is the most common protozoan parasite detected in stool samples, the major etiological agents of parasitic diarrhea are considered to be Cryptosporidium spp., Dientamoeba fragilis, Entamoeba histolytica, and Giardia intestinalis (22).E. histolytica is a pathogenic amoeboid protozoan parasite for which humans are the primary reservoir (27). It is a potentially invasive pathogen and the causative agent of amebiasis, with approximately 50 million cases and 100,000 deaths annually (28). The clinical presentation can range from asymptomatic carriage to gastrointestinal disease and invasive disease. E. histolytica is morphologically identical to the nonpathogenic species Entamoeba dispar and Entamoeba moshkovskii, though genetic differences have confirmed their separation into independent species (4, 20). Due to this conserved morphology, stained smears of stool specimens are insufficient for differentiation of the species. Currently, the only way to differentiate the pathogenic E. histolytica from the nonpathogenic strains via microscopy is to visualize ingested red blood cells within the E. histolytica trophozoite; however, this is rarely seen i...