The etiology of invasive bacterial infections was studied among 956 Filipino children less than five years old who fulfilled the World Health Organization criteria for severe or very severe pneumonia or had suspected meningitis or sepsis. The most common invasive infections were due to Streptococcus pneumoniae (12 [1.3%]) and Haemophilus influenzae (12 [1.3%]); including four cases of pneumococcal meningitis and 11 cases of H. influenzae meningitis. Type 1 was the most common (six of the 12 isolates) of the pneumococcal serotypes. Serotypes/groups 1, 6, 14, and 23 accounted for 91.7% of the invasive isolates. The majority of the H. influenzae strains from blood (10 out of 10) and cerebrospinal fluid (6 out of 7) were type b. Almost all of the invasive S. pneumoniae (9 out of 12) and H. influenzae (11 out of 12) infections were seen before one year of age, which stresses the need to investigate early immunization of children for H. influenzae type b and S. pneumoniae, as well as maternal immunization to maximize the potential of immunoprophylaxis.