The present transcript profiling compares the gene expression during cold-acclimation in different genotypes of barley (Hordeum vulgare L.), wheat (Triticum aestivum L.) and rye (Secale cereale L.) in order to determine factors influencing frost tolerance. Because of its outstanding robustness against adverse environmental conditions rye is considered to be a model species for abiotic stress tolerance. Wheat is moderate frost-tolerant and barley is most sensitive species in this study. The aim of this study elucidate conserved, as well as, species-specific gene regulation across the Triticeae. Furthermore, transcript abundances were correlated between the distinct frost tolerances of genotypes within each species in order to find candidate genes for frost tolerance. Overall design: Six winter-genotypes of each species with variable frost toleance (3 sensitive, 3 tolerant) were selected and cold-acclimated at 2°C under phytotron conditions. Sampling was done in the middle of photo period at day 0 (control), day 1, day 7 and day 21 of cold-acclimation. RNA's extracted from primary shoots of three biological replications were pooled. Cross-species transcript profiling was applied by using a barley unigene cDNA-macroarray comprising more than 12000 features, spotted in duplicate.