Microbiological findings in harbour porpoises from different regions of the North Atlantic were compared. Results in animals from the North and Baltic Seas were evaluated over a period of 18 years for changes in the microbiological flora. Microbiological investigations were performed on 1429 organ samples from the lung, liver, kidney, spleen, intestine, and mesenteric lymph nodes from harbour porpoises of the German North and Baltic Seas, Greenlandic, Icelandic and Norwegian waters. A large variety of bacteria, including potentially pathogenic bacteria like Brucella sp., Clostridium perfringens, Escherichia coli, Erysipelothrix rhusiopathiae, beta-haemolytic streptococci and Staphylococcus aureus were isolated. Those bacteria were associated with bronchopneumonia, gastroenteritis, hepatitis, pyelonephritis, myocarditis and septicemia. Organs from animals originating from Greenlandic and Icelandic waters showed clearly less bacterial growth and fewer associated pathological lesions compared to animals from the German North and Baltic Seas and Norwegian waters. Differences in bacterial findings and associated lesions between harbour porpoises from the German North and Baltic Seas and animals from Greenlandic, Norwegian and Icelandic waters may result from higher stress due to anthropogenic activities such as chemical pollutants in the North and Baltic Seas.