ABSTRACTBats are natural reservoirs of protozoal, viral, fungal and bacterial pathogens. However, little has been described about their endoparasites, especially in the Neotropics, despite the fact that this region represents a high taxonomic and functional bat diversity. In this study, we describe gastrointestinal parasites found in faecal samples of Neotropical bats from the Amazon rainforest of Colombia. We characterise the prevalence of parasites by employing flotation and McMaster techniques. We obtained 222 samples, but only 15 bats (6.8%) of the species Carollia brevicauda (n = 9), C. perspicillata (n = 3), Artibeus planirostris (n = 1), A. lituratus (n = 1) and Gardnerycteris crenulatum (n = 1) were positive for gastrointestinal parasites. This is the first survey of bat gastrointestinal parasites conducted in the Colombian Amazon. We report for the first time coccidian parasites in phyllostomid bats from Colombia. We also found nematodes in gestating females, which may suggest a transfer of parasites to the foetus during pregnancy in fruit bats. Besides insectivorous bats, frugivores can also represent a source for gastrointestinal parasites in the Neotropics, but the factors that determine their hosting capacity are still not fully understood. Further research should explore the interactions of wild and domestic hosts with parasites, which could be useful for analysing potential risks to the human population.KEYWORDS: Amazonian rainforestChiropteraendoparasitismhelminthprotozoa AcknowledgementsWe are in debt to the Amazon Institute of Scientific Research (SINCHI) Florence headquarters for economic and logistical support in agreement with contract no. SGR 218 of 2018 framed within the project Restauración de áreas disturbadas por implementación de sistemas productivos agropecuarios en el departamento del Caquetá, convenio 060/2013. We thank the owners of the farms who allowed us to carry out the samplings, for their kindness and hospitality. We are also grateful to Victor Fernando Santana-Lima for his help in the identification of parasites. Finally, we thank the editor and three anonymous reviewers who substantially improved the quality of this paper.Disclosure statementNo potential conflict of interest was reported by the authors.Additional informationFundingThis work was supported by the Instituto Amazónico de Investigaciones Científicas SINCHI [Convenio 060/2013 entre la gobernación del Caquetá].