Frequency of micronuclei (MN) and other nuclear abnormalities (nuclear buds, bi-nucleated and fragmented-apoptotic cells) was analysed in gill cells of the blue mussel (Mytilus spp.) from selected coastal sites in the Baltic Sea--Kvädöfjärden (Sweden), Klaipeda-Būtinge zone (Lithuania), Gulf of Gdansk (Poland) and Wismar Bay (Germany). Samples were collected from 650 specimens during bi-annual sampling campaigns in 2001 and 2002. The lowest frequency of MN (0.37 MN/1000 cells) was found in blue mussels from the reference site (Kvädöfjärden). The highest MN values (up to 6.7 MN/1000 cells) were registered in blue mussels from the Gulf of Gdansk in autumn 2001 and 2002, and at Wismar Bay in spring 2001 (up to 5.06 MN/1000 cells). Gradients of MN incidences were observed when comparing the three studied locations in Wismar Bay, and at the Lithuanian coast before the crude oil spill in the Būtinge oil terminal. Moreover, significant seasonal and inter-location differences in the responses were documented (P<0.0001). Nuclear abnormalities were observed most frequently in blue mussels from the Gulf of Gdansk.