Due to its highly parallel approach, DNA microarray technology opens up new possibilities that may be particularly beneficial for laboratory diagnosis of infectious diseases. We developed a microarray assay for detection and differentiation of all currently defined chlamydial species belonging to the genera Chlamydia and Chlamydophila using the ArrayTube system, which we found to be particularly user-friendly and economical. The test includes PCR amplification of a 23S rDNA target region with concurrent biotinylation and subsequent hybridisation in the ArrayTube, a micro-reaction tube carrying the microarray chip on the bottom. In addition to high specificity, the assay was shown to allow detection and genetic characterisation of single PCR-amplifiable target DNA copies.