Introduction: Streptococcus pneumoniae is a worldwide leading cause of morbidity and mortality, while susceptibility towards penicillin and macrolides can be less than 50% in many regions. Methodology: A total of 150 isolates of S. pneumoniae causative of invasive diseases in children were characterized, of which 24.6% had a fatal outcome. Results: The most prevalent serotypes were 19F, 6B, 23F and 14. Resistance to penicillin, erythromycin (mostly of macrolide-lincosamide-streptogramin resistance phenotype) or trimethoprim-sulfamethoxazole was found in more than 40% of the isolates, but no resistance phenotype appeared linked to lethality. Serotype 3 isolates, which were seldom resistant, had a twofold lethality rate compared to the total sample. Conclusion: Serotyping could provide a better outcome-predicting tool than susceptibility testing. The seven-valent vaccine does not include the most prevalent serotypes found in Mexico.