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Objective To describe and compare serotype distribution and antibiotic susceptibility of invasive and nasopharyngeal isolates of Streptococcus pneumoniae from children in rural Mozambique. Methods From August 2002 to July 2003, we prospectively obtained invasive pneumococcal isolates from children <15 years of age admitted to the paediatric ward of Manhiça District Hospital. During a cross-sectional study of children <5 years of age with mild illnesses, attending the outpatient department of the hospital in March and April 2003, we collected nasopharyngeal isolates. Serotypes and antibiotic susceptibilities were determined using standardized methods. Results The two most common pneumococcal serotypes among invasive isolates were types 1 (40% of 88 isolates serotyped) and 5 (10%), but these types were rare among nasopharyngeal isolates. Compared with invasive isolates, nasopharyngeal isolates were more likely to be serotypes in the licensed seven-valent conjugate vaccine (49% vs. 20%, P < 0.01), to have intermediate-level penicillin resistance (52% vs. 14%, P < 0.01) and to be non-susceptible to trimethoprim–sulfamethoxazole (61% vs. 45%, P < 0.01). Recent receipt of antibiotics or sulfadoxine/pyrimethamine were associated with carriage of antibiotic non-susceptible isolates. Conclusions These data indicate that a pneumococcal conjugate vaccine containing serotypes 1 and 5 could substantially reduce pneumococcal invasive disease among young children in rural Mozambique. Carriage surveys can overestimate potential coverage of the seven-valent pneumococcal conjugate vaccine in settings where serotypes 1 and 5 predominate. [ABSTRACT FROM AUTHOR]