In the Baltic Sea, studies regarding biological effects of contaminants are relatively few, partly due to political and economical reasons, specific hydrographic characteristics, and a strong eutrophication-targeted research focus during the past three decades. The development of a monitoring strategy concerning biological effects and its implementation into environmental monitoring programmes in the Baltic Sea is lagging behind the progress currently taking place in most of western and southern Europe. The pan-European project BEEP (Biological Effects of Environmental Pollution on Marine Coastal Ecosystems, 2001-2004) included the Baltic Sea as one of the target areas for the evaluation of a suite of biological effects indicators in European coastal waters. The main aims of the BEEP project are described and how the expected outcome for the Baltic Sea could provide the needed "baseline" information and expertise for a biological effect monitoring and contribute to harmonise environmental monitoring programmes within the EU.