Previous studies have shown a correlation between fluoroquinolone use in hospitals and rates of meticillin-resistant Staphylococcus aureus (MRSA) infection. This study examined the effect on MRSA infection rates within individual adult units of a tertiary care teaching hospital after instituting a programme to decrease ciprofloxacin use. Clinical specimens positive for S. aureus were determined on all adult inpatient units between 1 January 2004 and 31 December 2005. Units with >10 isolates of S. aureus per year were included in the analysis. Ciprofloxacin use, measured in defined daily doses per 1000 patient-days, was determined for each unit during the same time period. Ciprofloxacin use and MRSA rates for 2004 and 2005 were compared. In the 17 units studied, ciprofloxacin use decreased by 31.2% (P<0.0001). The MRSA rate in these units decreased from 59.6% to 54.2% (P=0.122). There was a correlation between ciprofloxacin use and the MRSA rate within these units (r=0.70; 95% confidence interval -0.01-0.94; P=0.053). Within individual units, there was a variable response. In seven of the units, there was an increase in the MRSA rate despite a reduction in ciprofloxacin use, suggesting that other factors (length of stay, infection control and community-acquired MRSA) may have contributed. Although many factors are associated with high MRSA rates, ciprofloxacin use appears to be a contributing factor. Reducing the use of ciprofloxacin may be a means of controlling MRSA in the hospital setting.