Nowadays, many commercial kits allowing the detection of digestive parasites by DNA amplification methods have been developed, including simplex PCR assays (SimpPCRa) allowing the identification of a single parasite, and multiplex PCR assays (MultPCRa) allowing the identification of several parasites at once. Thus, aimed at improving the diagnosis of intestinal protozoal infections, it is essential to evaluate the performances of these new tools. A total of 174 DNA samples collected between 2007 and 2017 were retrospectively included in this study. Performances of four commercial SimpPCRa (i.e., CerTest-VIASURETM) and three MultPCRa (i.e., CerTest-VIASURETM, FAST-TRACK-Diagnostics-FTD-Stool-ParasiteTM and DIAGENODE-Gastroenteritis/Parasite-panel-ITM) were evaluated for the detection of Cryptosporidium spp., Entamoeba spp., and Giardia intestinalis in stool samples compared to our routinely used in-house SimpPCRa. Globally, the SimpPCRa showed better sensitivity/specificity for the detection of G. intestinalis, E. histolytica, E. dispar, and Cryptosporidium spp. (i.e., 96.9/93.6%; 100/100%; 95.5/100%; and 100/99.3%, respectively), compared to the three commercial MultPCRa tested. All in all, we showed that MultPCRa offer an interesting alternative for the detection of protozoans in stool samples depending on the clinical context.