Until recently, the search for enteropathogens causing travellers' diarrhea was based on stool culture (Campylobacter spp., Salmonella spp. and Shigella spp.), direct microscopy with (Cryptosporidium spp.) or without specific staining (Giardia lamblia, Entamoeba histolytica) or specific antigen detection (Giardia lamblia, Entamoeba histolytica). Molecular analyses are progressively replacing traditional diagnostic methods but their clinical usefulness remains to be better defined. This article attempts to describe the advantages and disadvantages of these new molecular methods and to illustrate situations where they could be useful using clinical cases frequently encountered in the practice of travel medicine.