Development of transcriptome analysis methods such as differential display PCR and construction of subtractive libraries now makes it possible to profile gene expression in response to xenobiotic exposure. As an example of application of these methods, zebra mussels (Dreissena polymorpha) were treated with various contaminants such as Aroclor 1254, 3-methylcholanthrene, chrysene and atrazine. A total of 242 mRNAs were identified as differentially expressed. Analysis of these mRNAs should provide valuable information regarding detoxification mechanisms in this bivalve species. In addition, the use of cDNA array technology applied to these gene products may constitute a multi-marker approach to monitor the effect of contamination on this aquatic species.