Background: Ungulates from zoological institutions are frequently used as founders in reintroduction programmes. These animals are subject to specific parasite management as parasitic infections have previously been associated with failed Bovidae reintroductions. Methods: Questionnaires to obtain data on how these institutions screen for seasonal parasite presence and the clinical signs they induced in threatened ungulates were sent to 65 institutions involved in European Ex situ Programmes (58.5% response rate). Temperature and relative humidity data were also obtained to categorize each zoological centre. Results: Strongyloides spp. (52.6%), Trichuris spp. (42.1%), Trichostrongylidae family (39.4%) and Eimeria spp. (36.8%) were the most frequently reported parasites in the received questionnaires. Climatic variables did not influence parasite presence. Conclusion: Our results suggest that artificial microenvironments created by husbandry practices and enclosure design in zoos could create hotspots for gastrointestinal parasites. To maximise the success of reintroduction projects, we recommend that the influence of microclimates on parasite burdens be evaluated.