The expression levels of 96 genes were characterized and differentiated using a cDNA microarray after the bacterium Escherichia coli was exposed to numerous toxic chemicals. In all, the effects of 14 different chemicals and 1 mixture were investigated using 1-h exposure data to provide information about physiological changes brought on by the stress experienced and interaction of chemical-gene expression. Hierarchical clustering analysis showed that the genes could be sub-grouped based upon their expression patterns while each also showed unique signatures to each chemical tested when examined using a principal component analysis (PCA). By constructing a chemical-gene expression profiling based on changes in the expression of the genes for each chemical, we were able to identify the chemicals effects and gene targets more systematically. Despite the fact that only a small number of genes were used for gene expression analysis, they were sufficient to discriminate between the effects of each exposure. It was found that the use of a single time point for expression analysis was insufficient for interpreting the effects a given chemical has on the bacterium. Such information cannot be obtained from conventional toxicity studies, demonstrating that chemical-gene expression profiling method based on the hierarchical clustering analysis and principal component analysis (PCA) in toxicity monitoring offers a new perspective for bio-monitoring and information on dynamic changes occurring at the sub-cellular level. (c) 2006 Elsevier Ltd. All rights reserved.