Heavy metals are significant inorganic environmental pollutants. Brassica juncea, frequently used as model for phytoremediation studies, can (hyper)accumulate some heavy metals with well-developed root system. Even though the elucidation of the differentially expressed genes in response to heavy metals is important for the improvement of phytoremediation capacity of plants, there has been limited number of reports about detailed functional characterization of these genes. In this study, 50 mu M Pb(NO3)(2) and 25 mu M CdSO4 were applied separately to 31 days-old Brassica juncea (var. P78) plants for 24 h to identify the putative genes associated with lead (Pb) and cadmium (Cd) stress. The metal content analyses indicated that B. juncea (var. P78) is lead and cadmium hyperaccumulator. To reveal molecular mechanisms responsible for metal metabolism, the differentially expressed genes in the roots of Pb-treated plants were investigated by using the microarray chips of Arabidopsis thaliana probes (Affymetrix-The GeneChip Arabidopsis ATH1 Genome Array). Out of 183 differentially expressed genes in response to Pb stress, only 20 of the up-regulated and 18 of the down-regulated genes were statistically significant at p < 0.05. Since most of 38 genes differentially expressed under Pb stress were interspecifically very well conserved, we concluded that the use of interspecific hybridization approaches for global gene expression profiling would be limited. The interspecific usability of the probes was further tested by determining the level of conservation between Arabidopsis microarray oligo and Brassica spp. sequences. The microarray results were validated by quantifying the level of expression of six important genes, which are likely to play a role in Pb metabolism, through quantitative RT-PCR. To further pinpoint the possible role of Pb stress response genes, the expression of these genes at different tissues of the plants after Pb and Cd treatments were measured. In conclusion, the described genes are likely to be associated with Pb and Cd stress metabolism and provide potential targets for the improvement of phytoremediation capacity in plants.