We report on a sensitive, specific and easy to interpret PCR based diagnostic tool for the detection of Schistosoma japonicum eggs in the faeces of infected mammalian hosts. Primer pairs were designed to amplify regions of the mitochondrial DNA of the parasite. The specificity of the PCR primers was tested using either faecal samples from non-infected hosts or hosts infected with the related schistosome species S. mansoni. Sensitivity was investigated in a study, which differentiated the presence or absence of eggs in faecal samples. PCR results were correlated with analysis of the samples by microscopy. PCR analysis provided a level of sensitivity of 87.7%, while specificity was 100%. The PCR-based assay could detect mitochondrial DNA from as little as 0.3 of a single egg. The overall detection threshold of the PCR test was >or=60 eggs per gram of faeces. Advantages of this technique include the ability to scale-up screening and the reproducibility and simplicity of interpretation of results compared with standard microscopic methods.