The effect of recalcitrant soil and water pollutant 2,4,6-trinitrotoluen (TNT) on gene expression in Arabidopsis thaliana rosettes and roots was studied separately for the first time using microarrays. Seven-day exposure to TNT resulted in 170 up- and 122 down-regulated genes in the rosettes and 61 up- and 51 down-regulated genes in the roots (expression difference > 1.5-fold; p[t test] < 0.05). TNT concentration, 5 µg/ml, was selected according to the dose response analysis and study of TNT uptake from liquid media. Although many TNT induced genes fell into ontology groups annotated as response to biotic and abiotic stresses in rosettes and roots, only a small overlap of TNT effects on transcriptome was observed between rosettes and roots. The rosettes exhibited induction of several genes associated with toxin metabolism, such as UDP-glycosyltransferases and ATP-binding cassette (ABC) family transporters. On the other side, no genes known to be involved in TNT transformation were found to be up-regulated in the roots. The genes coding for enzymes involved in the cell wall modifications were abundantly up-regulated in roots. Microarray data indicated that after a relatively long incubation with TNT (7 days), metabolism of this xenobiotic proceeded mainly in aerial parts, while its translocation into cell walls still took place in the roots. Results obtained by microarray hybridization were validated by quantitative real-time reverse-transcription PCR. Nitrate reductase 1, several glycosyltransferases and ABC transporters, sucrose-proton symporter 2, thioredoxin-dependent peroxidase 2, and gamma-glutamyltransferase are discussed for their potential to enhance detoxification and toleration capability of plants to TNT.