Bacteremias represent severe infectious complications following hematopoietic stem cell transplantation (HSCT). Frequency is highest during the pre-engraftment period, both in autologous and in allogeneic HSCT, when patients are granulocytopenic. In the postengraftment period, bacteremias are also frequent in the absence of neutropenia, especially after allogeneic HSCT. Antibacterial prophylaxis with fluoroquinolones during pre-engraftment neutropenia could be justified both in autologous and allogeneic HSCT, but the possibility of infections caused by resistant pathogens should be carefully evaluated. Empirical antibacterial therapy must be chosen on the basis of local epidemiology and should be administered in all febrile HSCT recipients, regardless of the presence of neutropenia. This approach appears to be justified by the high incidence of bacteremia in any post-transplant period and by the high mortality rate that is observed if appropriate treatment is delayed, especially in infections caused by specific pathogens (e.g., Gram-negative rods).