Light microscopy of thick and thin blood smears is the mainstay of malaria diagnosis. In situations of low-level parasitaemia such as drug-modified disease, however, this may be difficult making clinical management problematic. Polymerase chain reaction (PCR) methods have shown high sensitivity for the diagnosis of malaria and are able to differentiate the Plasmodium species involved. Two cases are presented in the present study, which illustrate how a PCR method can aid light microscopic malaria diagnosis and species differentiation in returned travellers with low-level parasitaemia. Plasmodium vivax was detected by PCR prior to the light microscopy becoming positive in one case, and in the second case Plasmodium malariae was detected when light microscopy was unable to speciate the causative Plasmodium species.