Cryptosporidium parvum mainly invades the intestinal epithelium and causes watery diarrhea in humans and calves. However, the invasion process has not yet been clarified. In the present study, the invasion process of C. parvum in severe combined immunodeficiency (SCID) mice was examined. Infected mice were necropsied; the ilea were double-fixed routinely and observed by scanning and transmission electron microscopy. In addition, the microvillus membrane was observed by ruthenium red staining. Scanning electron micrographs showed elongation of the microvilli at the periphery of the parasite. The microvilli were shown to be along the surface of the parasite in higher magnification. Transmission electron microscopy confirmed that the invading parasites were located among microvilli. Parasites existed in the parasitophorous vacuole formed by the microvillus membrane. The parasite pellicle attached to the host cell membrane at the bottom of the parasite, and then the pellicle and host cell membrane became unclear. Subsequently, the pellicle became complicated and formed a feeder organelle. In addition, invasion of the parasite was not observed in either a microvillus or the cytoplasm of the host cell. Therefore, C. parvum invades among microvilli, is covered with membranes derived from numerous microvilli, and develops within the host cell.