The use of PCR-based molecular diagnosis in travel medicine remains limited to specific indications such as clinical suspicion of some of the viral hemorrhagic fevers (e.g. Ebola, Marburg), differential diagnosis between Entamoeba histolytica (pathogen) and E. dispar (non pathogen) in the stools, and parasitological diagnosis of cutaneous leishmaniasis. The scope of indications is likely to expand in the coming years with the development of techniques (e.g. multiplex PCR) able to identify several pathogens from a single sample. Simplification and cost-reduction of molecular techniques, which would allow for more equitable access to these diagnostic tools in countries where the targeted diseases are highly prevalent, pose major technological and ethical challenges.