Malaria is a common, life-threatening infection in endemic tropical areas and one that presents a diagnostic challenge to laboratories in most non-endemic countries. A rapid and accurate diagnosis is a prerequisite for effective treatment, especially for the potentially fatal cases of Plasmodium falciparum infection. In the present, multi-centre study, the performances of a rapid diagnostic test (NOW) Malaria) and several, commercial, PCR-based assays (AMS61, AMS42, AMS43, AMS4 and AMS45) were compared against the results of microscopical examination of bloodsmears (the current 'gold standard'). The subjects were either non-European immigrants (N=135) or international travellers (N=171). There was good concordance between the results of all the detection methods, with kappa values of >0.8. Although the NOW Malaria rapid test was both sensitive (100%) and specific (100%) in detecting P. falciparum infections, it was less specific (93.1%) and sensitive (90.7%) in identifying the other Plasmodium species. The results from the AMS61 assay, designed to detect any malarial infection, generally parallelled those of the microscopy (kappa = 0.89), giving a specificity of 98.2% and a sensitivity of 91.0%. Although the use of species-specific molecular primers to identify pure infections with P. falciparum and P. vivax gave results that were in good agreement with those of the microscopy, the subjects who had apparently pure infections with P. ovale or P. malariae were always found PCR-negative. Compared with the standard microscopy, both the NOW Malaria test and the PCR-based assays were therefore poor at identifying mixed infections. The NOW Malaria test and the PCR-based assays clearly need to be improved, particularly for the correct identification of infections with Plasmodium spp. other than P. falciparum, including mixed infections. For now, expert microscopy must remain the mainstay of the laboratory diagnosis of malaria.