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A nested polymerase chain reaction (PCR) method that uses genus- and species-specific primers was evaluated for a field study in Burkina Faso and for routine diagnosis of imported malaria in France. The results were compared to those of microscopical diagnosis. The overall parasite index was 17.5% (7 of 40) by PCR assay, compared with 12.5% (5 of 40) by microscopical examination of thick smears of field samples. By contrast, the overall parasite index was 35% (14 of 40) by both PCR and thin smear microscopical examination of blood from imported cases. The nested PCR assay is a powerful tool for epidemiological studies of malaria prevalence in endemic area. It is not however more sensitive than conventional microscopy for routine diagnosis of imported malaria. The interpretation of our results is as following: very low parasitaemias that are undetectable by microscopy are frequently observed in endemic areas, however, symptomatic imported malaria cases are associated with higher patent parasitaemias.