European flounders from two UK estuaries with different contaminant profiles were sampled and analysed for impacts of PAHs, heavy metals and estrogenic compounds by currently adopted measurement procedures used in statutory monitoring programs. These showed that fish from the polluted Tyne estuary had responded to all three classes of pollutants with elevations in hepatic EROD, MT and plasma VTG and that there was considerable interanimal variation in the magnitude of the response. Analysis of PAH metabolites in bile showed recent uptake of low molecular weight PAHs. The pollutant response was also apparent when hepatic levels of cytochrome P450 1A (CYP1A), metallothionein (MT) and vitellogenin (VTG) mRNAs were quantified by real time PCR. Whilst there did not appear to be a direct correlation between levels of gene transcripts and their protein products on an individual basis, these results demonstrate that measurements of mRNA levels of specific genes, or their protein products both demonstrate induction in polluted environments and are thus valid measures in biomonitoring studies. Procedurally, the use of the single generic technology of Q-PCR was much simpler and is worth pursuing in future studies.