Summary:Effective prophylaxis against specific infections has allowed increasingly potent conditioning regimens to be given, thereby prolonging survival in HSCT recipients. The Centers for Disease Control and Prevention, in collaboration with numerous professional societies, has recently published guidelines to codify and advance this approach. Controversy remains in several areas but, curiously, the most intense debate concerns prevention of bacterial infections, the most extensively studied of all of the approaches. Central to this debate are the competing priorities of a potentially ill patient on the one hand vs the long-term consequences of unchecked antibiotic use. The emergence in the 1990s of vancomycin-resistant Enterococcus demonstrated all too vividly how devastating such an end result could be. This article will review the arguments for and against the routine use of antibacterial prophylaxis in HSCT recipients.