We developed a case-control study in order to identify risk factors associated with pharyngeal colonization by Streptococcus pneumoniae with reduced susceptibility to fluoroquinolones (ciprofloxacin MIC, >4 g/ml). A total of 400 patients were studied for colonization by quinolone-nonsusceptible S. pneumoniae (QNSP) isolates and risk factors for this colonization. Isolate susceptibility was determined by the agar dilution method. Forty patients were colonized by QNSP (case patients), and 360 patients were not colonized by QNSP (control patients). The MIC range of ciprofloxacin for QNSP isolates was 4 to 8 g/ml. No isolates were resistant to levofloxacin and moxifloxacin. Risk factors significantly associated with QNSP colonization, according to univariate analysis, were recent hospitalizations (odds ratio [OR], 3.43; 95% confidence interval [CI], 1.6 to 7.2; P < 0.01) and prior exposure to fluoroquinolones (OR, 6.04; 95% CI, 3.0 to 12.0; P < 0.01). Other factors such as chronic obstructive pulmonary disease (OR, 1.94; 95% CI; 0.7 to 5.0), prior exposure to penicillins (OR, 1,68; 95% CI, 0.8 to 3.3) and prior exposure to macrolides (OR 2; 95% CI, 0.6 to 6.2) were more frequent among patients colonized with QNSP, but there was no statistical significance. Multivariate analysis showed that exposure to fluoroquinolones was the only independent factor associated with colonization by QNSP (OR, 4.2; 95% CI, 1.8 to 9.4; P < 0.01). Throat colonization by QNSP is becoming frequent, though most of these isolates (all the isolates in this case) remain susceptible to newer fluoroquinolones. Previous treatment with fluoroquinolones seems to be the main risk factor associated with colonization by QNSP.The emergence and spread of drug-resistant Streptococcus pneumoniae are a major cause of concern in pneumococcal infection in recent years. More than 50% of isolates now found in several countries are resistant to penicillin (1,7,13,14,25), with Spain as one of the countries with the highest penicillin resistance rates (18). Among penicillin-resistant S. pneumoniae isolates, 60 to 80% are also resistant to cefuroxime, erythromycin, and clindamycin (13). Since the release in the late 1990s of newer fluoroquinolones (FQs) with enhanced activity against pneumococci, these drugs have been prescribed with increasing frequency for initial treatment of respiratory tract infections (10,22). FQ resistance rates remain low in S. pneumoniae in most countries (3,6,17), though higher resistance rates have been reported occasionally in some countries (9,12).Recent studies have shown that 30% of S. pneumoniae isolates for which the ciprofloxacin (CIP) MIC is 4 g/ml, and virtually all pneumococcal isolates for which the CIP MIC is Ͼ4 g/ml harbor one or more topoisomerases mutations (2), though not all these strains are levofloxacin (LEV) or moxifloxacin (MOX) resistant. Another recent study (16) showed that 59% of S. pneumoniae isolates intermediate for LEV (MIC of 2 g/ml) have a first-step mutation in parC. Thus, this group of strains with reduc...