Sixty four episodes of bacteraemia that appeared during antimicrobial prophylaxis with an oral quinolone plus an azole in neutropenic cancer patients were compared with 128 cases of bacteraemia in a cohort of controls matched for age, sex, underlying disease, neutropenia and vascular catheter in situ to assess differences in aetiology, cost of therapy and outcome. Patients who received prophylaxis had breakthrough bacteraemias of a different aetiology compared with the control group: they had significantly fewer multiply-resistant strains (21.9 vs. 51.5, P<0.04) and a longer afebrile neutropenic period (9.55 days vs. 4.1, P<0.001). Patients who received prophylaxis also had bacteraemias that were significantly more frequently caused by viridans streptococci (9.4% vs. 1.7%, P<0.01), enterococci (15.6% vs. 7.2%, P<0.05) and Stenotrophomonas maltophilia (17.2% vs. 3.4%, P<0.01). The cost of antimicrobial therapy per case (37 401 SKK (1091 USD) vs. 31 808 SKK (899 USD), P<0.05) was also significantly higher in cases than controls; however, the number of administred antibiotics (4.18 vs. 3.21 per case, P=NS) was similar in both groups. There were no differences in outcome between both groups. However patients who received prophylaxis had significantly longer periods of afebrile neutropenia (9.55 days vs. 4.1, P<0.001) and bacteraemia developed later than in controls. Also, the incidence of polymicrobial bacteraemia caused by multiresistant strains was lower among cases (21.9 vs. 51.5, P<0.04).