Harbour porpoises (Phocoena phocoena) are useful indicators of the health of their wild populations and marine ecosystems, yet their elusive nature makes studying them in their natural environment challenging. Stranded porpoises provide an excellent source of data to study the health and biology of these animals and identify causes of death, diseases and other threats. The aim of this study was to document pathology, and where possible, cause of death in porpoises from Swedish waters. Post-mortem examinations were performed on 128 stranded porpoises collected from 2006 to 2020. Overall, bycatch including definitive and probable cases was the most common cause of death (31.4%), followed by disease (21.3%), predominantly pneumonia. In adults, infectious disease was the most common cause of death. Bacteria with zoonotic potential such as Erysipelothrix rhusiopathiae and Brucella sp. were documented for the first time in porpoises from Swedish waters, as was the porpoise-adapted group B Salmonella enterica ST416/ST417. Three of four deaths from non-infectious diseases involved parturition complications. Four cases of suspected predation were documented, but further analyses are required to confirm these findings. Our results are consistent with those from other regions in Europe and serve as a reference for future monitoring for changing patterns of health and disease of porpoises and their environments.