A microarray hybridization assay for identification of chlamydiae was developed using the ArrayTube platform. The technology is comparatively inexpensive and involves plastic tube-integrated microchips and signal amplification by enzyme-catalyzed silver precipitation. Hybridization probes were designed on the basis of the most variable window approach, which identified species-specific nucleotide polymorphisms in a region of generally high sequence similarity. The selected 26-nt probe sequences were used on two different series of customized microarrays, i.e. combinatorial high-density in situ synthesized arrays and low-density spotted arrays. Target DNA was prepared by consensus PCR amplifying a 1-kbp segment of the ribosomal RNA operon. Unique species-specific hybridization patterns were obtained for all nine species of the family Chlamydiaceae on both microarray types. The present assay proved suitable for unambiguous species identification of chlamydial cell cultures and showed a potential for direct detection of these bacteria from clinical tissue.