Black-necked swans are distributed across South America and face conservation problems in Chile according to data of the State institution SAG. The aim of this study was to identify helminths and to assess associated tissue damage via histopathology. A total of 19,291 parasites were isolated from 21 examined birds; 17 species were identified, including nematodes, flukes, and tapeworms. Of these, 12 were new host records, 13 were reported for the first time in Chile, and 5 were new records for the Neotropical region. Further, the flukes Schistosomatidae gen. sp. and Echinostoma echinatum are of zoonotic concern. Regarding histopathology, an inflammatory response was found along the birds’ entire digestive tract. Nevertheless, it is difficult to declare that there is a clear association between such lesions and isolated parasites, as other noxa could be responsible as well. Although in some cases there was an evident association, such inflammatory responses and necrosis were minimal, as occurred with Capillaria, Retinometra, Catatropis, Echinostoma, and Schistosomatidae gen. sp. Nevertheless, Epomidiostomum vogelsangi caused granulomatous injuries, an important inflammatory response, and necrosis, but it always circumscribed to superficial layers of the gizzard. Conversely, Paramonostomum was not associated with an inflammatory response despite a high parasitic load.