Intestinal infection by the coccidian parasite Cryptosporidium is a well-recognized condition in immunocompromised hosts and in some normal persons. The authors studied a patient with acquired immunodeficiency syndrome and cryptosporidiosis of the small intestine. The parasite inhabits the microvillous brush border of the intestinal epithelium and must be carefully sought on light microscopic examination of intestinal biopsy specimens. Characteristic life cycle stages are observed on electron microscopy. The absence of significant light microscopic alterations of the villous architecture in this patient's biopsy specimen and in other cases suggests that other factors, such as toxin elaboration by cryptosporidia or other organisms, may be involved in the pathogenesis of diarrhea. Abnormal aggregation of lysosomes at the apices of intestinal epithelial cells may reflect ineffective host phagocytic mechanisms.