Zoonotic diseases are transmitted between animals and humans by direct or indirect contact (OIE, 2019). It has been reported that 60% of infectious agents are zoonotic and that 75% of emerging infectious diseases are of animal origin (OIE, 2019), these diseases can be caused by viruses, bacteria, fungi or parasites, among the latter we find Cryptosporidium spp., an obligate intracellular protozoan parasite, belonging to the phylum apicomplexa causative agent of cryptosporidiosis, a great importance diarrheal disease for public health because there have been multiple outbreaks worldwide; Among the main species of Cryptosporidium that have been reported as causing cryptosporidiosis in humans are C. parvum and C. hominis. Taking into account its migration to urban and peri-urban areas, it is necessary to evaluate its possible role in the disease transmission to humans. Therefore the aim of this investigation was determine the presence of Cryptosporidium spp., in bats from the Macaregua cave, Santander, Colombia. For this purpose 80 samples of bat intestine of Carollia perspicillata, Natalus tumidirrostris and Mormoops megalophylla species were selected from this cave. Subsequently, DNA extraction of the selected intestines was performed and a PCR was performed for the cytochrome b (Cyt-b) gene in order to verify the quality of the extracted DNA. After this, a semi-nested PCR for the 18S rRNA gene was carried out in order to determine the presence of Cryptosporidium spp, in the extracted DNA, however, it was not possible to visualize the expected band for Cryptosporidium spp. Because of this, it was decided to perform a real-time PCR (qPCR) for the 18S rRNA gene with the purpose of confirming or ruling out the parasite presence. As a result of the 80 DNA samples extracted, 78.75% (n = 63), were positive for the cytochrome b (Cyt-b) gene, in the semi-nested PCR no positivity was detected, while in the qPCR 5 positive samples were identified. Then, it was determined the presence of Cryptosporidium spp., in 7.94% of the total analyzed samples however, it is necessary continue investigations to clarify the Cryptosporidium species present in bats and thus contribute to understanding the bats role in the spread and transmission of Cryptosporidium to humans and other domestic or farm animals.