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<p>Abstract</p> <p>Background</p> <p>The study describes the molecular epidemiology of <it>Streptococcus pneumoniae </it>causing invasive disease in Gambian children</p> <p>Methods</p> <p>One hundred and thirty-two <it>S. pneumoniae </it>isolates were recovered from children aged 2–29 months during the course of a pneumococcal conjugate vaccine trial conducted in The Gambia of which 131 were characterized by serotyping, antibiotic susceptibility, BOX-PCR and MLST.</p> <p>Results</p> <p>Twenty-nine different serotypes were identified; serotypes 14, 19A, 12F, 5, 23F, and 1 were common and accounted for 58.3% of all serotypes overall. MLST analysis showed 72 sequence types (STs) of which 46 are novel. eBURST analysis using the stringent 6/7 identical loci definition, grouped the isolates into 17 clonal complexes and 32 singletons. The population structure of the 8 serotype 1 isolates obtained from 4 vaccinated and 2 unvaccinated children were the same (ST 618) except that one (ST3336) of the isolates from an unvaccinated child had a novel ST which is a single locus variant of ST 618.</p> <p>Conclusion</p> <p>We provide the first background data on the genetic structure of <it>S. pneumoniae </it>causing IPD prior to PC7V use in The Gambia. This data will be important for assessing the impact of PC7V in post-vaccine surveillance from The Gambia.</p>