Between 1996 and 2005 the carcasses of 355 harbour seals originating from the coast of Schleswig-Holstein, Germany, were investigated for pathological changes. The animals were collected before (n=280) and after (n=75) the second phocine distemper virus (PDV) epizootic in 2002. The seals were either found dead or were killed due to severe illness. Necropsy was performed in each case, in addition to histopathological, immunohistochemical, microbiological and parasitological examinations. Throughout the period of study, the respiratory and alimentary tracts were the organ systems most consistently affected by pathological change. The most common cause of death was bronchopneumonia caused by parasitic and/or bacterial infection of the lung. Less frequently identified changes included: trauma, gastroenteritis, uterine torsion or dystocia, polyarthritis/polymyositis, intestinal torsion, septicaemia, dermatitis, and keratitis. The most frequent causes of bronchopneumonia, gastroenteritis, polyarthritis, dermatitis and septicaemia were infections with alpha/beta-haemolytic streptococci, Escherichia coli and Clostridium perfringens. A number of changes were more frequently identified after 2002. These included the presence of parasites in the lung, stomach and intestine; bronchopneumonia, gastritis, enteritis, septicaemia and perinatal death. The increased prevalence of these changes may have been related to the preceding PDV epidemic.