The Arabidopsis transcriptome was studied using the Affymetrix Arabidopsis ATH1 GeneChip in wild-type plants and glufosinate-tolerant transgenic plants expressing the bialaphos resistance (bar) gene. Pleiotropic effects were specifically generated in the transcriptomes of transgenic plants by both the bar gene and glufosinate treatments. In the absence of glufosinate, four genes were differentially expressed in the transgenic lines and another 80 genes were differentially expressed in the presence of glufosinate, 29 of which were specific to transgenic plants. In contrast, the number of differentially expressed genes specific to wild-type plants was 194 during the early response at 6 h of glufosinate treatment, and increased to 3711 during the late response at 48 h. Although the wild-type plants undergo extensive transcriptional reprofiling in response to herbicide-induced stress and, finally, plant death, the transgenic plants appear to activate other detoxification processes to offset the toxic effects of the residual herbicide or its derivatives. This study provides the first description of the pleiotropic effects of the bar gene and glufosinate on the plant transcriptome.