Exposure to radiation induces a reduction in the number of gastrointestinal, anaerobic bacterial flora, and an increase in the number of Enterobacteriaceae that are associated with sepsis and mortality. Antimicrobials that suppress anaerobic flora have a deleterious effect on survival by promoting earlier enterobacterial sepsis. In contrast, in studies of animals and immunosuppressed patients, antimicrobials that inhibit gram-negative enteric bacteria and preserve the anaerobic flora have shown a beneficial effect by preventing bacterial translocation and fatal sepsis. The quinolone antimicrobials hold potential for therapy of endogenous and exogenous infection after irrodiation.