Using a neonatal mouse model of Cryptosporidium parvum infection, we investigated whether apoptosis of epithelial cells was induced in the small intestine. At the time when the number of C. parvum oocysts in the ileum was maximal, columnar goblet cells and absorptive cells showed a decrease in the ileal epithelium that was accompanied by a significant reduction in the height of the villi. A few apoptotic epithelial cells were also observed in the vicinity of the basal crypts where C. parvum was proliferating. Morphological changes of the villous structure and apoptotic epithelial cells associated with proliferation of the parasite were scarcely detected in the duodenum, cecum, and colon of the infected mice. These findings suggest that the loss of absorptive cells and goblet cells, and the apoptosis of intestinal epithelial cells, are common events in the ileum after C. parvum infection, and that epithelial apoptosis may have a significant role in the pathogenesis of cryptosporidiosis.