We monitored the modifications of oral and intestinal microfloras of 10 allogeneic bone marrow recipients who received randomly either norfloxacin or pefloxacin (400 mg three times a day) as selective decontamination for infection prevention. After 1 week of treatment, in all patients members of the family Enterobacteriaceae were no longer detectable and in all but one pefloxacin-treated patient enterococci were also eliminated in the intestine. The anaerobic flora was not affected, with the exception of Bacteroides spp., markedly reduced after treatment with pefloxacin. In most patients the most striking effect was the increase in staphylococcal counts. These strains were found to be resistant to both quinolones in the study. Less consistent changes were observed in oral flora. No relevant difference could be demonstrated between the two regimens on bacterial counts either in feces or in saliva. This study shows the efficacy of both quinolones in eradicating gram-negative bacilli in the alimentary tract of bone marrow transplant patients; however, the finding of the overgrowth of resistant gram-positive organisms during treatment with these agents deserves further evaluation.