Three methods for the extraction of polycyclic aromatic hydrocarbons (PAHs) from zebra mussels (Dreissena polymorpha) sampled from Hamilton Harbour were compared. Replicate freeze-dried mussel tissue samples were extracted using acid digestion, tissue homogenization (mechanical extraction) and ultra-sonication. Each extract was submitted to a cleanup procedure (alumina chro-matography and Sephadex LH20 gel chromatography), followed by analysis using gas chromatography-mass spectrometry (GC-MS). The three extraction methods were equally efficient, based on a statistical comparison of mean concentrations of individual PAHs. Mussel extracts, when subjected to bioassays with Salmonella typhimurium strain YG1029 (TA100-like) in the presence of an exogenous metabolic activation system (S9), exhibited significant mutagenic responses; these responses varied with the PAH content of the mussel extracts. Sources of PAHs in mussel extracts were determined by examining the profiles of sulfur-containing polycyclic aromatic compounds (thia-arenes). Comparison of the ratios of certain thia-arenes with ratios in source samples enabled identification of vehicular emissions and coal tar-contaminated sediment as two sources of PAH contamination in Hamilton Harbour.