Objective: To investigate the presence of neutrophil extracellular traps (NETs) in vivo by analysing intestinal sections from experimentally Eimeria bovis- and naturally Eimeria arloingi-infected animals. Methods: Intestinal samples of Eimeria arloingi- and Eimeria bovis-infected animals were analysed by using immunohistochemical and fluorescence approach by using monoclonal antibodies. Results: Classical NET components were confirmed by co-localization of extracellular DNA being decorated with neutrophil elastase and histones in Eimeria-infected tissue samples. Here, extrusion of NETs was exclusively detected in intestinal polymorphonuclear neutrophils infiltrating Eimeria-infected sites. In vivo NETs were either found in close proximity or in direct contact to different Eimeria stages suggesting a stage-independent process. NETs were also found within the gut lumen driven by polymorphonuclear neutrophils that were contacting released oocysts. Conclusions: We postulate that NETs might play an important role in innate defence reactions in coccidiosis therefore significantly altering the outcome of infection.