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Objective  Efficient and easy-to-use DNA extraction and purification methods are critical in implementing PCR-based diagnosis of pathogens. In order to optimize the routine clinical laboratory diagnosis of eukaryotic enteric pathogens, we compare, via quantitative PCR cycle threshold (Ct) values, the efficiency of two DNA extraction kits: the semi-automated EZ1 ®  (Qiagen) and the manual QIAamp ®  DNA Stool Mini Kit (Qiagen), on six protozoa:  Blastocystis  spp.,  Cryptosporidium parvum / hominis ,  Cyclospora cayetanensis ,  Dientamoeba fragilis ,  Giardia intestinalis  and  Cystoisospora belli  and one microsporidia:  Enterocytozoon bieneusi .    Results  Whereas EZ1 ®  (Qiagen) and QIAamp ®  DNA Stool Mini Kit (Qiagen) yielded similar performances for the detection of  Cryptosporidium  spp. and  D. fragilis , significant lower Ct values (p < 0.002) pointed out a better performance of EZ1 ®  on the five remaining pathogens. DNA extraction using the semi-automated EZ1 ®  procedure was faster and as efficient as the manual procedure in the seven eukaryotic enteric pathogens tested. This procedure is suitable for DNA extraction from stools in both clinical laboratory diagnosis and epidemiological study settings.

Evaluation of two DNA extraction methods for the PCR-based detection of eukaryotic enteric pathogens in fecal samples