Most hematogenous candidiasis originates from endogenous host flora. The impact of clinically prominent Candida colonization on short-term mortality (<or=14 weeks) was prospectively studied in 193 hospitalized patients from 1998 to 1999. Clinically prominent colonization included yeasts isolated from all sterile body sites and >50 colonies of Candida from non-sterile sites. Fourteen (7.1%) patients were granulocytopenic (ANC <or=100/microl). Nineteen (9.8%) had undergone marrow transplantation, 26 (13.5%) had a hematologic malignancy and 129 (66.5) had non-hematologic cancer. Candida isolates (216) were collected form 210 specimens. Fifty-three (27.5%) patients died; 25 (19.4%) with solid tumors, compared to 16 (61.5%) with hematological malignancy, and 11 (57.9%) BMT recipients (P < 0.001). No deaths were seen in patients with AIDS, and one (7.7%) in a patient with a benign condition (P < 0.001). Twenty-six (29.2%) patients with respiratory tract, 13 (23.2%) with gastrointestinal tract, and three (14.3%) with genitourinary tract colonization died. In patients with multiple-site colonization, mortality was significantly higher (45.5%) (P < 0.05). Mortality was higher in patients with C. glabrata (52.9%) and C. krusei (75%) colonization than with C. albicans (24.1%) (P < 0.025). This study shows that patients with hematologic cancer and recipients of marrow transplant with Candida colonization of multiple body sites, and colonization with C. glabata or C. krusei have poor survival.