The emergence of fluoroquinolone-resistant gram-negative organisms has been demonstrated in patients given fluoroquinolone prophylaxis. To prevent increases in resistant bacteria, we restricted prophylactic use of fluoroquinolones. The spectrum and susceptibility patterns of isolates causing bloodstream infection (BSI) were assessed in patients receiving chemotherapy during periods of routine prophylaxis (period A: October 2001 to May 2003) and restricted prophylaxis (period B: June 2003 to January 2005). The total number of patients receiving chemotherapy was 442 during period A and 365 during period B. No significant differences were seen between periods with respect to patient characteristics. BSI was identified in 42 patients (44 episodes) during period A and 69 patients (74 episodes) during period B. Incidence of BSI increased significantly from 10.0% (44/442) during period A to 20.3% (74/365) during period B (P < 0.0001). Rate of Enterobacteriaceae BSI increased significantly, from 2.0% (9/442) during period A to 8.2% (30/365) during period B (P < 0.0001). For all BSI episodes, the proportion of BSI with gram-positive cocci decreased from 63.6% (28/44) during period A to 44.6% (33/74) during period B (P = 0.045), while the proportion of BSI with Enterobacteriaceae increased from 20.5% (9/44) to 40.5% (30/74) (P < 0.0001). The proportion of fluoroquinolone-resistant Enterobacteriaceae BSI for all Enterobacteriaceae BSI decreased from 75% (9/12) during period A to 17% (5/30) during period B (P = 0.0078). Restriction of fluoroquinolone prophylaxis affects the etiology of BSI and reduces the proportion of drug-resistant organisms.