Annual investigations of the health status of female perch (Perca fluviatilis) were performed during 8-13 years in order to detect long-term, large-scale changes in the Baltic Sea. These background data are also meant to be used as baselines in recipient investigations at various point sources in the Baltic Sea. Fish were sampled at three coastal sites in Sweden: two in the Baltic Proper (since 1988) and one in the Bothnian Bay (since 1993). In all, 19 biochemical, physiological and histopathological variables were measured. By reflecting central functions of life, such as red blood cell functions, immune defence, liver function, biotransformation processes, intermediary metabolism, ion balance, and reproduction, the selected variables give a good picture of the health status of the fish. The most important observations were strong trends towards decreased gonadosomatic index (relative gonad size) and increased hepatic EROD activity in female perch in the Baltic Proper. Most of the other variables varied little between the years. The reduced gonad size and the EROD induction indicate that factors in the environment, e.g. the occurrence of pollutants, affect important physiological functions, such as reproduction and biotransformation processes, in fish even in a reference area in the Baltic Proper. It is urgent to make further studies in order to identify which pollutant(s) or other possible cause(s) are responsible for the observed biological effects.