Background: Intestinal protozoan infection is one of the main causes of gastrointestinal diseases. Protozoa are usually detected by direct smear microscopy, concentration techniques, or special stains; however, these techniques are labor-intensive and require well-trained technicians. Therefore, molecular techniques involving polymerase chain reaction (PCR) have been developed to satisfy the need for unbiased and rapid analytical methods with high sensitivity and specificity. In this study, the BD MAX TM Enteric Parasite Panel (EPP) (Becton, Dickinson and Company, USA), designed to detect Cryptosporidium parvum and/or hominis, Giardia lamblia, and Entamoeba histolytica, and the Allplex TM Gastrointestinal Parasite Assays (AGPA) (Seegene Inc., Korea), designed to detect Cryptosporidium species, G. lamblia, E. histolytica, Blastocystis hominis, Dientamoeba fragilis, and Cyclospora cayetanensis were compared to determine whether any of these assays could become a useful tool for detecting intestinal protozoan infections in Korea. Methods: We investigated 295 fecal samples using EPP and AGPA. Then we confirmed the positive results with the conventional and nested PCR. Consistent detection by conventional PCR, nested PCR, and one of the multiplex panels was considered "true positive." Results: Out of 295 samples, 17 were true positives for B. hominis and 2 were true positives for E. histolytica. EPP detected parasites in only two samples owing to its design; however, its true positive detection rate was 100% (2/2). AGPA detected parasites in 24 samples with 79.2% (19/24) true positives. Conclusions: The incidence of protozoan, especially B. hominis, infection may be more prevalent than expected. AGPA could be an effective tool for screening protozoan infections.