Commercially farmed European flounder (Platichthys flesus) were treated with benzo[a]pyrene or cadmium under controlled laboratory conditions. In addition, animals were collected from the polluted Tyne and relatively clean Alde estuaries in the UK. Potential differentially expressed genes were isolated from liver tissue by means of suppressive, subtractive hybridisation. A total of 284 different mRNAs were identified as having the potential for being differentially expressed, of which 84 could be tentatively identified by homology with database sequences. These clones will form part of a flounder cDNA array for validation and future applications, with full identification being pursued for those expressed sequence tags for which differential expression can be confirmed by array technology. (C) 2004 Published by Elsevier Ltd.