The present study investigated fecal flora changes in 20 patients who received either the nonabsorbable antifungal agent amphotericin B, or the absorbable antifungal agent flluconazole, with tobramycin and vancomycin as preparation for undergoing allogeneic bone marrow transplantation (BMT). The oral antibiotic regimen consisted of tobramycin (540 mg/day, three times a day), vancomycin (1, 500 mg/day, three times a day) and either amphotericin B (2, 400 mg/day, twice a day) (AMPH group) or fluconazole (400 mg/day, twice a day) (FLCZ group) and was designed to prevent infections from microorganisms in the gut. Aerobic bacterial colonies were not detected on the day of BMT or 1 week after BMT, except in 1 case unable to take the full antibiotic regimen due to nausea and vomiting. Anaerobic bacterial colonies were not detected on the day of BMT except in this single case. Furthermore, there were no episodes of bacterial infection. In both groups, Candida colonies were detected in some case. Candida colonies were also detected in the pharynx and urine. However, there were no fungal infections. The present report suggests that amphotericin B and fluconazole administrations, with tobramycin and vancomycin, are equally effective for protection against bacterial and fungal infections in BMT recipients.