A female Cuvier’s Beaked Whale (Ziphius cavirostris) specimen measuring 580 cm in length died after being stranded in Southeastern Brazil. Following a necropsy, organ samples were obtained, fixed in 10% neutral buffered formalin and histopathologically analyzed. A severe and generalized hypodermis infection by Phyllobothrium delphini (Phyllobothriidae) was observed, resulting in granulomatous panniculitis. Severe renal and arterial lesions were also noted, including a severe bone metaplasia in the aorta artery, associated with a massive infection by Crassicauda sp, (Tetrameridae). A significant thoracic hemorrhage due to thoracic aorta artery rupture was noted, also likely due to this infection, resulting in a fatal injury. This study contributes towards knowledge on histopathologic changes in the scarcely studied Cuvier’s Beaked Whale, is the first to associate a Crassicauda sp. infection in this whale species in the Brazilian region and also the first to indicate a resulting osseous metaplasia due to this parasitism and granulomatous dermatitis associated with Phyllobothrium delphini. Furthermore, this is also, to the best of our knowledge, the first report of Phyllobothrium delphini cysts in a Ziphius cavirostris specimen to date.