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Autopsies carried out on stranded harbour porpoises provide an opportunity to assess health problems in this species. We performed 61 autopsies on live-stranded harbour porpoises, which died following admission to a rehabilitation centre between 2003 and 2016. The animals had stranded on the Dutch (<jats:italic>n<\/jats:italic>\u2009=\u200952) and adjacent coasts of Belgium (<jats:italic>n<\/jats:italic>\u2009=\u20092) and Germany (<jats:italic>n<\/jats:italic>\u2009=\u20097). We assigned probable causes for stranding based on clinical and pathological criteria. Cause of stranding was associated in the majority of cases with pathologies in multiple organs (<jats:italic>n<\/jats:italic>\u2009=\u200929) compared to animals with pathologies in a single organ (<jats:italic>n<\/jats:italic>\u2009=\u200918). Our results show that the three most probable causes of stranding were pneumonia (<jats:italic>n<\/jats:italic>\u2009=\u200935), separation of calves from their mother (<jats:italic>n<\/jats:italic>\u2009=\u200910), and aspergillosis (<jats:italic>n<\/jats:italic>\u2009=\u20099). Pneumonia as a consequence of pulmonary nematode infection occurred in 19 animals. Pneumonia was significantly associated with infection with <jats:italic>Pseudalius inflexus, Halocercus<\/jats:italic> sp., and <jats:italic>Torynurus convolutus<\/jats:italic> but not with <jats:italic>Stenurus minor<\/jats:italic> infection. Half of the bacterial pneumonias (6\/12) could not be associated with nematode infection. Conclusions from this study are that aspergillosis is an important probable cause for stranding, while parasitic infection is not a necessary prerequisite for bacterial pneumonia, and approximately half of the animals (29\/61) probably\u00a0stranded due to multiple causes. An important implication of the observed high prevalence of aspergillosis is that these harbour porpoises suffered from reduced immunocompetence.<\/jats:p>","DOI":"10.1186\/s13567-019-0706-3","type":"journal-article","created":{"date-parts":[[2019,10,30]],"date-time":"2019-10-30T23:03:14Z","timestamp":1572476594000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":23,"title":["Clinical, pathological, and laboratory diagnoses of diseases of harbour porpoises (Phocoena phocoena), live stranded on the Dutch and adjacent coasts from 2003 to 2016"],"prefix":"10.1186","volume":"50","author":[{"given":"Cornelis E.","family":"van Elk","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marco W. G.","family":"van de Bildt","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter R. W. 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