(Uploaded by Plazi for the Bat Literature Project) ABSTRACT. Bats are potential reservoirs of Cryptosporidium and Eimeria. The genus Cryptosporidium infects various vertebrates and causes a diarrheal disease known as cryptosporidiosis. Many epidemiological studies in wild animals have been performed; however, most of them relied on only PCR-based detection because of the difficulty of performing pathological analyses. Accordingly, the natural host and pathogenicity of Cryptosporidium bat genotypes remain unclear. In this study, we captured Eptesicus nilssonii (Northern bats) in Hokkaido, Japan. Of the three intestinal samples obtained, two were positive for Cryptosporidium spp. and one was positive for Eimeria spp. The corresponding microorganisms were also confirmed histopathologically. We detected the novel Cryptosporidium bat genotype XII and Eimeria rioarribaensis in bat intestine.