Abstract Invasive species negatively influence the biodiversity of the ecosystems they invade and may introduce pathogens to native species. Raccoon dogs have very successfully invaded Europe, including, recently, Denmark. This study included analyses of gastrointestinal helminths and Trichinella spp. from 99 raccoon dogs and 384 native red foxes collected from October 2009 to March 2012. The sedimentation and counting method used revealed that raccoon dogs and foxes harboured 9 and 13 different helminth species, respectively, of which several known to be zoonotic. Significantly more nematode and cestode species were found in foxes while raccoon dogs had more trematode species. Rodent transmitted parasites were more prevalent in foxes, while amphibian transmitted parasites were more prevalent in raccoon dogs. One fox was infected with Echinococcus multilocularis (0.3%), while no Trichinella spp. were detected in raccoon dogs or foxes. The trematode Brachylaima tokudai was detected for the first time in Denmark in five of 384 foxes (1.3%). Prevalences of Pygidiopsis summa (3.0% and 3.4%) and Cryptocotyle spp. (15.2% and 15.4%) were comparable in raccoon dogs and foxes, respectively. Four helminth species were more prevalent in foxes than in raccoon dogs: Toxocara canis (60.9% and 13.1%); Uncinaria stenocephala (84.1% and 48.5%); Mesocestoides spp. (42.7% and 23.2%); and Taenia spp. (30.7% and 2.0%), respectively. Three helminth species were more prevalent in raccoon dogs than in foxes: Dipylidium caninum (5.1% and 0.3%); Mesorchis denticulatus (38.4% and 4.2%); and Alaria alata (69.7% and 34.4%), respectively. T. canis was more abundant in foxes while A. alata was more abundant in raccoon dogs. The intestinal distribution of a number of helminth species was comparable between hosts, but highly variable between parasite species. Inherent biological factors and host invasion of new areas might have shaped these marked differences in helminth fauna between the invasive raccoon dog and the native red fox.