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The parasitological examination of stools is a challenging analysis due to the diversity of parasites to be screened for, which depends on the exposure context and the patient’s clinical background. Parasite detection is traditionally performed using direct wet mount and various concentration methods followed by microscopic reading, which requires expertise. The official billing code for this stool test in the French nomenclature of medical biology procedures has become outdated due to the development of molecular biology techniques and observed epidemiological changes. Nucleic acid detection techniques currently on the market, often in multiplex panels, should not be used without an understanding of their limitations in terms of the relevance of the parasite panel detected and their technical performance. These recommendations aim to guide biologists and COFRAC auditors in selecting techniques and implementing parasitological stool examinations, taking into account their limitations, in order to ensure optimal medical care.