Patients undergoing bone marrow transplantation become immuno-compromised for various reasons. Deep granulocytopenia, induced by conditioning (chemotherapy and total body irradiation), renders the patient at risk for serious bacterial and fungal infections. Our strategy for prevention of these infections by selective decontamination (SD) is the result of more than 15 years of clinical experience and research. The combination of antibiotics, used as standard SD (neomycin, polymyxin B, pipemidic acid and amphotericin B), with the application of local antimicrobial agents eliminates aerobic Gram-negative rods, Staphylococcus aureus and Candida spp. from the mucosal surfaces of the digestive tract, while the majority of the anaerobic flora persist and support colonization resistance (CR). The antibiotics used either are not resorbed or do not yield therapeutic serum concentrations. Antibiotics which induce therapeutic serum concentrations, such as ciprofloxacin and cotrimoxazole, are only used for SD on a limited scale. When Gram-negative rods persist despite intake of the standard regimen, ciprofloxacin is given until these persisting rods are eliminated. If the patients cannot swallow the oral regimen, i.v. cotrimoxazole is given temporarily. Streptococcal infections are prevented by the i.v. adminstration of penicillin for 14 days starting on the first day after cytotoxic treatment (conditioning for bone marrow transplantation). The combination of SD and systemic prophylaxis has been shown to be adequate; the major problem then remaining is a relatively mild catheter-associated infection with coagulase-negative staphylococci.