Background: Penicillin and third generation cephalosporin resistant pneumococcal isolates have emerged in Chile, mainly in the pediatric population. These isolates complicate therapeutic alternatives, specially among patients with central nervous system infections. Aim: To assess the frequency of penicillin and third generation cephalosporin resistance among isolates obtained from pediatric patients with invasive pneumococcal infections, and to study serotypes and clinical risk factors associated with resistance. Material and methods: Microbiological isolates obtained from children between April 1994 and May 1999 with pneumococcal invasive infections, were serotyped and analyzed according to their susceptibility to penicillin and cefotaxime by E-test and broth microdilution testing. Potential risk factors studied included patient's age, previous antibiotic use or admissions, comorbidity, and serotypes. Results: Seventy eight patients were studied. Penicillin-resistant pneumococcal isolates were detected in 35.9% of cases (21.8% with intermediate and 14.1% with high level resistance) without significant variation among different clinical conditions. Most of the high level penicillin-resistant pneumoccocal isolates had MIC ≥4 µg/mL (8 out of 11 strains). One third of penicillin-resistant isolates also expressed cefotaxime resistance. Multivariate analysis indicated an age ≤36 months (OR=6.8; IC 95%: 1.4 to 33.5) and serotype 14 (OR=6.3; IC 95%: 1.7 to 23.3) as factors associated with penicillin resistance. Conclusions: One third of the invasive pneumococcal isolates obtained from pediatric patients were resistant to penicillin. Risk factors involved a younger age and pneumococcal isolates belonging to serotype 14 (Rev Méd Chile 2002; 130: 26-34)