| Summary: | Diagnostic approaches based on PCR methods are increasingly used in the field of parasitology, particularly to detect <i>Cryptosporidium</i>. Consequently, many different PCR methods are available, both “in-house” and commercial methods. The aim of this study was to compare the performance of eight PCR methods, four “in-house” and four commercial methods, to detect <i>Cryptosporidium</i> species. On the same DNA extracts, performance was evaluated regarding the limit of detection for both <i>C. parvum</i> and <i>C. hominis</i> specificity and the ability to detect rare species implicated in human infection. Results showed variations in terms of performance. The best performance was observed with the FTD<sup>®</sup> Stool parasites method, which detected <i>C. parvum</i> and <i>C. hominis</i> with a limit of detection of 1 and 10 oocysts/gram of stool respectively; all rare species tested were detected (<i>C. cuniculus, C. meleagridis, C. felis, C. chipmunk</i>, and <i>C. ubiquitum</i>), and no cross-reaction was observed. In addition, no cross-reactivity was observed with other enteric pathogens. However, commercial methods were unable to differentiate <i>Cryptosporidium</i> species, and generally, we recommend testing each DNA extract in at least triplicate to optimize the limit of detection.
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