We investigated (1) the prevalence and quantity of, as well as risk factors for, orointestinal Candida colonization in patients undergoing hematopoietic stem-cell transplantation (HSCT) and (2) the genetic relatedness of colonizing C. albicans strains. Mouth-wash and stool samples were collected from 77 patients before they underwent HSCT and on days 1, 8, and 15 and were quantitatively cultured. C. albicans isolates were genotyped by microsatellite-marker analysis. The prevalence and quantity of orointestinal Candida colonization varied over time. In 48% (13/27) of multicolonized patients, the same Candida genotype was present in oral and intestinal samples. Oral colonization and decontamination of the gut by vancomycin and paromomycin were risk factors for intestinal Candida colonization.