Resistance to penicillin and multiple antimicrobial agents among Streptococcus pneumoniae strains is becoming an increasing problem worldwide and in Asia. To determine the prevalence of carriage of S. pneumoniae isolates not susceptible to penicillin in young children, we obtained nasopharyngeal swab specimens from 1,978 children (ages, 2 to 6 years) attending 79 day care centers or kindergartens. Three hundred eighty-three strains of S. pneumoniae were isolated from these children. Fifty-eight percent of these isolates had reduced susceptibility to penicillin, 123 (32.1%) were intermediate, and 100 (26.1%) were resistant. A very high penicillin MIC (4 microg/ml) was found in 3.3% of the isolates. The isolates also demonstrated high rates of resistance to other antimicrobial agents (51.2% to cefaclor, 50.2% to cefuroxime, 42.8% to cefotaxime, 80.7% to trimethoprim-sulfamethoxazole, 77% to erythromycin, 60% to clindamycin, and 33.7% to chloramphenicol). No isolate was resistant to fluoroquinolone. Multidrug resistance (not susceptible to the beta-lactams and three or more other classes) was found in 39.4% of the isolates. Risk factors for the carriage of S. pneumoniae not susceptible to penicillin were multiple physician visits in the preceding 3 months and use of antimicrobial agents by the individual or by household members in the preceding 3 months. In the logistic regression analysis, only the use of antimicrobial agents in the preceding 3 months was an independent risk factor (P = 0.004; odds ratio, 2; 95% confidence interval, 1.2 to 3.2). This study demonstrated the high prevalence of antibiotic-resistant S. pneumoniae in healthy young children in the community in Hong Kong.