Objectives: To compare rates of in vitro fluoroquinolone resistance of bacterial isolates obtained from inpatients of two haematology-oncology services with high and low fluoroquinolone consumption. Methods: Two hospitals with consistently high (A) and low (B) fluoroquinolone use in their haematology-oncology services between the years 1999 and 2002 were identified in a hospital antibiotic use surveillance project. Rates of in vitro resistance to fluoroquinolones in inpatients of the services were determined for Escherichia coli and coagulase-negative staphylococcal bloodstream isolates, and also for Pseudomonas aeruginosa and Staphylococcus aureus isolates from any site. Results: Fluoroquinolone resistance of E. coli was significantly higher in hospital A than in hospital B, but there was no such correlation between fluoroquinolone use and resistance rates for P. aeruginosa and staphylococci. Conclusion: The impact of antibiotic consumption on the prevalence of resistance may differ widely between different pathogens. Interventions using ecological analyses of the relationship between hospital antibiotic use and resistance need to consider pathogen-specific dynamics in the emergence and control of bacterial resistance.