Thermotolerance is induced by moderated heat acclimation. Suspension cultures of heat-acclimated Arabidopsis thaliana L. (Heynh.), ecotype Columbia, show thermotolerance against lethal heat shock (9 min, 50 degrees C), as evidenced by a chlorophyll assay and fluorescein diacetate staining. To monitor the genome-wide transcriptome changes induced by heat acclimation at 37 degrees C, we constructed an A. thaliana cDNA microarray containing 7,989 unique genes, and applied it to A. thaliana suspension-culture cells harvested at various times (0.5, 1, 2.5, 6, and 16 h) during heat acclimation. Data analysis revealed 165 differentially expressed genes that were grouped into ten clusters. We compared these genes with published and publicly available microarray heat-stress-related data sets in AtGenExpress. Heat-shock proteins were strongly expressed, as previously reported, and we found several of the up-regulated genes encoded detoxification and regulatory proteins. Moreover, the transcriptional induction of DREB2 (dehydration responsive element-binding factor 2) subfamily genes and COR47/rd17 under heat stress suggested cross-talk between the signaling pathways for heat and dehydration responses.