It has recently been emphasized that high levels of inorganic and organic micropollutants (particularly organometals, POPs and PAHs) may be present in coastal waters at high latitudes, stressing the need to evaluate the effects of contaminants on marine organisms from sub-arctic zones. With this aim, specimens of the blue mussel Mytilus edulis were sampled in polluted and reference areas along the south-west coast of Iceland in July 2004. Samples were collected from the intertidal zone at three sites in Reykjavik harbour which are differently exposed to contaminants, and at three reference coastal sites, two located along the Reykjanes Peninsula and the third one on the northern part of Hvalfjordur fiord. Lipofuscin content, neutral lipid accumulation and lysosomal enlargement were evaluated in digestive cells from cryostat sections of the mussel hepatopancreas, and quantified by automated image analysis. Metallothionein induction was also determined in the same tissue. Results indicate that mussels from the inner part of Reykjavik harbour, which is the most sheltered and most influenced by extensive shipping traffic, were the worst affected, with the highest values in neutral lipids, lipofuscin and lysosomal swelling. At the other two harbour sites, mussels exhibited lower values, similar to those observed in organisms collected in Hvalfjordur fiord and in bay of Osar. Mussels from Kuagerdi had the lowest values.