Ciprofloxacin-susceptible (n = 7) and -resistant (MIC >or=4 mg/L) (n = 15) clinical isolates of Streptococcus pneumoniae from diverse sources in Hong Kong were studied for target site modifications and efflux phenotype. Reserpine-inhibited efflux of ciprofloxacin and/or levofloxacin was common in both susceptible and non-susceptible isolates. The ParC substitutions K137N and/or S79F or Y were associated with increased ciprofloxacin MICS. The GyrA substitution S81F was only found in isolates with full resistance to ciprofloxacin (MIC >or=16 mg/L) and levofloxacin (MIC >or=8 mg/L). Among clinical isolates of S. pneumoniae, accumulation of target site mutations in strains with an efflux mechanism was associated with increasing MICs of fluoroquinolones.