Eimeria species (>1700) are widespread causative agents of coccidiosis in animals. Most species reproduce in the intestinal epithelial cells of distinct hosts. Eimeria falciformis infects the cecum of Mus musculus for its asexual and sexual reproduction. Parasite infection results in diarrhea and weight loss, and pathogenicity depends on the dose of infection as well as the age and immune status of the host. The short, monoxenous life cycle of E. falciformis in a model host (i.e., mouse) enables in vivo research on poorly studied coccidian stages. Several parasite-specific biological phenomena, such as schizogony, gametogenesis, oocyst formation, sporulation. and mucosal immunity can be examined in significant detail. The Eimeria–mouse model is valuable for deciphering the network design principles and molecular determinants of intracellular parasitism, and thereby developing novel antiparasitic intervention strategies against poultry and livestock coccidiosis caused by host-specific Eimeria species.