Two patients undergoing bone marrow transplantation developed severe gastrointestinal symptoms, one during the peri-transplantation period and the other several months post-transplantation and following documented intestinal graft-versus-host disease. After detection of Giardia lamblia trophozoites in a stool specimen from one patient and a duodenal aspirate from the other, treatment with metronidazole was administered and all symptoms resolved. Giardiasis should be considered in transplant patients with diarrhea. Negative stool examinations do not rule out this possibility, and consideration should be given to examining a sample of small intestinal contents for Giardia trophozoites.